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/7921153/working' mkdir: created directory `/scratch/stefan/7921153/working/protonate' Storing results in /scratch/stefan/7921153/finished Working in /scratch/stefan/7921153/working /scratch/stefan/7921153/working /scratch/stefan/7921153 /scratch/stefan/7921153/working/protonate /scratch/stefan/7921153/working /scratch/stefan/7921153 Precomputing protomers for all compounds (pH: 7.4) rm: cannot remove `/nfs/home/stefan/.install4j': No such file or directory rm: cannot remove `/nfs/home/stefan/.install4j': No such file or directory rm: cannot remove `/nfs/home/stefan/.install4j': No such file or directory mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory ph 7.4: 1029 protomers created Coalesing and merging protomers 1003 protomers generated for 1000 compounds Checking for new stereocenters and expanding 1003 protomers after new stereo-center expansion /scratch/stefan/7921153/working /scratch/stefan/7921153 Bulk generating 3D conformations all protomers in /scratch/stefan/7921153/working/3D mkdir: created directory `/scratch/stefan/7921153/working/3D' We are using corina for 3D embeding debuging info:: /scratch/stefan/7921153/working/protonate/xaaaaae-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' 1004 3D conformations generated for 1000 compounds Building REAL250005041893 mkdir: created directory `/scratch/stefan/7921153/working/building' mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041893' /scratch/stefan/7921153/working/building/REAL250005041893 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041893 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041893/0 /scratch/stefan/7921153/working/building/REAL250005041893 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 1) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/1 `/scratch/stefan/7921153/working/3D/1' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC(=O)NC1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005041893.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041893.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041893/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041893 none C=CCC(=O)NC1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 121, 121, 121, 59, 59, 59, 21, 9, 21, 1, 9, 1, 1, 1, 1, 1, 1, 59, 201, 201, 201, 201, 201, 121, 59, 59, 59, 59, 21, 21, 21, 1, 59, 59] 201 rigid atoms, others: [33, 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, 34, 35]) total number of confs: 809 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041893 none C=CCC(=O)NC1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 37, 37, 59, 59, 59, 59, 59, 1, 55, 55, 55, 36, 36, 6, 1, 1, 1, 1, 11, 11, 11, 59, 1, 1] 201 rigid atoms, others: [34, 35, 5, 6, 7, 8, 9, 19, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33]) total number of confs: 315 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041893 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041893 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 mkdir: created directory `/scratch/stefan/7921153/finished' Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041893/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041893 Building REAL250005041894 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041894' /scratch/stefan/7921153/working/building/REAL250005041894 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005041894 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041894/0 /scratch/stefan/7921153/working/building/REAL250005041894 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 2) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/2 `/scratch/stefan/7921153/working/3D/2' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)C1=CC(=O)[N-]O1)C1CC(NC(=O)C[NH+](C)C)C1) `REAL250005041894.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041894.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041894/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041894 none CN(C(=O)C1=CC(=O)[N-]O1)C1CC(NC(=O)C[NH+](C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 8, 1, 11, 5, 9, 6, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 188 conformations in input total number of sets (complete confs): 188 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 20, 20, 60, 60, 60, 60, 60, 1, 1, 1, 1, 6, 6, 6, 36, 38, 38, 38, 1, 8, 8, 8, 60, 1, 1, 1, 1, 6, 36, 36, 38, 38, 38, 38, 38, 38, 1, 1] 188 rigid atoms, others: [1, 39, 40, 10, 11, 12, 13, 21, 26, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 237 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041894 none CN(C(=O)C1=CC(=O)[N-]O1)C1CC(NC(=O)C[NH+](C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 8, 1, 11, 5, 9, 6, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 188 conformations in input total number of sets (complete confs): 188 using faster count positions algorithm for large data unique positions, atoms: [31, 10, 1, 10, 1, 1, 1, 1, 1, 1, 31, 60, 60, 60, 140, 140, 140, 188, 188, 188, 188, 60, 31, 31, 31, 1, 60, 60, 60, 60, 140, 188, 188, 188, 188, 188, 188, 188, 188, 60, 60] 188 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 25] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 661 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041894 /scratch/stefan/7921153/working /scratch/stefan/7921153 mkdir: created directory `1' /scratch/stefan/7921153/working/building/REAL250005041894/1 /scratch/stefan/7921153/working/building/REAL250005041894 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 1 (index: 3) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/3 `/scratch/stefan/7921153/working/3D/3' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CC(=O)NC1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005041894.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005041894.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041894/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041894 none CN(C)CC(=O)NC1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 149, 149, 149, 64, 64, 64, 20, 8, 20, 1, 8, 1, 1, 1, 1, 1, 1, 64, 201, 201, 201, 201, 201, 201, 201, 201, 149, 64, 64, 64, 64, 20, 20, 20, 1, 64, 64] 201 rigid atoms, others: [37, 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, 38, 39]) total number of confs: 725 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041894 none CN(C)CC(=O)NC1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 33, 6, 6, 6, 1, 1, 1, 1, 1, 11, 11, 39, 39, 64, 64, 64, 64, 64, 1, 33, 33, 33, 33, 33, 33, 28, 28, 6, 1, 1, 1, 1, 11, 11, 11, 64, 1, 1] 201 rigid atoms, others: [32, 33, 38, 6, 7, 8, 9, 10, 39, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37]) total number of confs: 247 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041894 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041894 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 1: /scratch/stefan/7921153/working/building/REAL250005041894/1.* 0: /scratch/stefan/7921153/working/building/REAL250005041894/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041894 Building REAL250005041895 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041895' /scratch/stefan/7921153/working/building/REAL250005041895 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041895 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041895/0 /scratch/stefan/7921153/working/building/REAL250005041895 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 4) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/4 `/scratch/stefan/7921153/working/3D/4' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)C1=CC(=O)[N-]O1)C1CC(NC(=O)CC#N)C1) `REAL250005041895.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041895.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041895/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041895 none CN(C(=O)C1=CC(=O)[N-]O1)C1CC(NC(=O)CC#N)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.1', 'N.1', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 8, 1, 11, 5, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 21, 21, 55, 55, 55, 55, 55, 1, 1, 1, 1, 6, 6, 6, 53, 53, 1, 9, 9, 9, 55, 1, 1, 1, 1, 6, 53, 53, 1, 1] 201 rigid atoms, others: [32, 1, 10, 11, 12, 13, 19, 24, 25, 26, 27, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 20, 21, 22, 23, 28, 29, 30]) total number of confs: 268 number of broken/clashed sets: 23 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041895 none CN(C(=O)C1=CC(=O)[N-]O1)C1CC(NC(=O)CC#N)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.1', 'N.1', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 8, 1, 11, 5, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 8, 1, 8, 1, 1, 1, 1, 1, 1, 23, 55, 55, 55, 135, 135, 135, 201, 201, 55, 23, 23, 23, 1, 55, 55, 55, 55, 135, 201, 201, 55, 55] 201 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 23] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 725 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041895 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041895 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041895/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041895 Building REAL250005041896 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041896' /scratch/stefan/7921153/working/building/REAL250005041896 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041896 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041896/0 /scratch/stefan/7921153/working/building/REAL250005041896 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 5) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/5 `/scratch/stefan/7921153/working/3D/5' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)C1=CC(=O)[N-]O1)C1CC(NC(=O)C2CC2F)C1) `REAL250005041896.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041896/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041896 none CN(C(=O)C1=CC(=O)[N-]O1)C1CC(NC(=O)C2CC2F)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 8, 1, 11, 5, 5, 5, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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] 0 hydrogens 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, 43, 108, 189, 189, 201, 201, 201, 201, 201, 43, 43, 11, 11, 1, 11, 1, 1, 1, 1, 43, 108, 108, 108, 201, 43, 43, 43, 43, 11, 1, 1, 1, 1, 43, 43] 201 rigid atoms, others: [32, 33, 14, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35]) total number of confs: 567 number of broken/clashed sets: 57 ./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: REAL250005041896 none CN(C(=O)C1=CC(=O)[N-]O1)C1CC(NC(=O)C2CC2F)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 8, 1, 11, 5, 5, 5, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 24, 24, 62, 62, 62, 62, 62, 1, 1, 1, 1, 6, 6, 6, 43, 43, 43, 1, 7, 7, 7, 62, 1, 1, 1, 1, 6, 43, 43, 43, 43, 1, 1] 201 rigid atoms, others: [1, 34, 35, 10, 11, 12, 13, 20, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 29, 30, 31, 32, 33]) total number of confs: 209 number of broken/clashed sets: 57 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041896 none CN(C(=O)C1=CC(=O)[N-]O1)C1CC(NC(=O)C2CC2F)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 8, 1, 11, 5, 5, 5, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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] 0 hydrogens 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, 9, 1, 9, 1, 1, 1, 1, 1, 1, 27, 62, 62, 62, 132, 132, 132, 201, 201, 201, 62, 27, 27, 27, 1, 62, 62, 62, 62, 132, 201, 201, 201, 201, 62, 62] 201 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 24] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 621 number of broken/clashed sets: 57 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041896 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041896 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041896/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041896 Building REAL250005041897 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041897' /scratch/stefan/7921153/working/building/REAL250005041897 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041897 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041897/0 /scratch/stefan/7921153/working/building/REAL250005041897 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 6) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/6 `/scratch/stefan/7921153/working/3D/6' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)C1=CC(=O)[N-]O1)C1CC(NC(=O)CCF)C1) `REAL250005041897.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041897/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041897 none CN(C(=O)C1=CC(=O)[N-]O1)C1CC(NC(=O)CCF)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 8, 1, 11, 5, 5, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 19, 19, 46, 46, 46, 46, 46, 1, 1, 1, 1, 6, 6, 6, 46, 76, 1, 8, 8, 8, 46, 1, 1, 1, 1, 6, 46, 46, 76, 76, 1, 1] 201 rigid atoms, others: [1, 34, 33, 10, 11, 12, 13, 19, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 20, 21, 22, 23, 28, 29, 30, 31, 32]) total number of confs: 402 number of broken/clashed sets: 19 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041897 none CN(C(=O)C1=CC(=O)[N-]O1)C1CC(NC(=O)CCF)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 8, 1, 11, 5, 5, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 7, 1, 7, 1, 1, 1, 1, 1, 1, 20, 46, 46, 46, 114, 114, 114, 201, 201, 46, 20, 20, 20, 1, 46, 46, 46, 46, 114, 201, 201, 201, 201, 46, 46] 201 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 23] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 727 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041897 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041897 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041897/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041897 Building REAL250005041898 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041898' /scratch/stefan/7921153/working/building/REAL250005041898 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041898 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041898/0 /scratch/stefan/7921153/working/building/REAL250005041898 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 7) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/7 `/scratch/stefan/7921153/working/3D/7' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H](C)C(=O)NC1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005041898.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041898.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041898/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041898 none CO[C@H](C)C(=O)NC1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [93, 93, 76, 93, 93, 76, 76, 34, 34, 34, 18, 7, 18, 1, 7, 1, 1, 1, 1, 1, 1, 34, 93, 93, 93, 93, 93, 93, 76, 34, 34, 34, 34, 18, 18, 18, 1, 34, 34] 93 rigid atoms, others: [36, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 322 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041898 none CO[C@H](C)C(=O)NC1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [33, 26, 6, 26, 26, 6, 6, 1, 1, 1, 1, 1, 6, 6, 18, 18, 34, 34, 34, 34, 34, 1, 33, 33, 33, 26, 26, 26, 6, 1, 1, 1, 1, 6, 6, 6, 34, 1, 1] 93 rigid atoms, others: [32, 37, 38, 7, 8, 9, 10, 11, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36]) total number of confs: 173 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041898 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041898 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041898/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041898 Building REAL250005041899 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041899' /scratch/stefan/7921153/working/building/REAL250005041899 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041899 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041899/0 /scratch/stefan/7921153/working/building/REAL250005041899 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 8) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/8 `/scratch/stefan/7921153/working/3D/8' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](O)C(=O)NC1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005041899.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041899.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041899/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041899 none C[C@@H](O)C(=O)NC1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [201, 172, 201, 201, 172, 172, 88, 88, 88, 29, 10, 29, 1, 10, 1, 1, 1, 1, 1, 1, 88, 201, 201, 201, 603, 172, 88, 88, 88, 88, 29, 29, 29, 1, 88, 88] 603 rigid atoms, others: [33, 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, 34, 35]) total number of confs: 1276 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041899 none C[C@@H](O)C(=O)NC1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [46, 6, 46, 46, 6, 6, 1, 1, 1, 1, 1, 11, 11, 42, 42, 88, 88, 88, 88, 88, 1, 46, 46, 46, 138, 6, 1, 1, 1, 1, 11, 11, 11, 88, 1, 1] 603 rigid atoms, others: [34, 35, 6, 7, 8, 9, 10, 20, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 30, 31, 32, 33]) total number of confs: 460 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041899 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041899 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041899/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041899 Building REAL250005041900 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041900' /scratch/stefan/7921153/working/building/REAL250005041900 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041900 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041900/0 /scratch/stefan/7921153/working/building/REAL250005041900 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 9) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/9 `/scratch/stefan/7921153/working/3D/9' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C1CC1C(=O)NC1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005041900.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041900.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041900/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041900 none C=C1CC1C(=O)NC1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 33, 33, 33, 23, 23, 23, 18, 7, 18, 1, 7, 1, 1, 1, 1, 1, 1, 23, 64, 64, 64, 64, 64, 33, 23, 23, 23, 23, 18, 18, 18, 1, 23, 23] 64 rigid atoms, others: [34, 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, 35, 36]) total number of confs: 189 number of broken/clashed sets: 5 ./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: REAL250005041900 none C=C1CC1C(=O)NC1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [30, 30, 30, 6, 6, 6, 1, 1, 1, 1, 1, 4, 4, 11, 11, 23, 23, 23, 23, 23, 1, 30, 30, 30, 30, 30, 6, 1, 1, 1, 1, 4, 4, 4, 23, 1, 1] 64 rigid atoms, others: [35, 36, 6, 7, 8, 9, 10, 20, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34]) total number of confs: 116 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041900 none C=C1CC1C(=O)NC1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 13, 13, 13, 30, 30, 30, 36, 36, 58, 58, 64, 64, 64, 64, 64, 30, 1, 1, 1, 1, 1, 13, 30, 30, 30, 30, 36, 36, 36, 64, 30, 30] 64 rigid atoms, others: [0, 1, 2, 3, 4, 21, 22, 23, 24, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 191 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041900 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041900 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041900/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041900 Building REAL250005041901 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041901' /scratch/stefan/7921153/working/building/REAL250005041901 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041901 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041901/0 /scratch/stefan/7921153/working/building/REAL250005041901 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 10) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/10 `/scratch/stefan/7921153/working/3D/10' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC1C(=O)NC1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005041901.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041901.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041901/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041901 none CC1=CC1C(=O)NC1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 119, 119, 47, 47, 47, 20, 8, 20, 1, 8, 1, 1, 1, 1, 1, 1, 47, 201, 201, 201, 201, 201, 119, 47, 47, 47, 47, 20, 20, 20, 1, 47, 47] 201 rigid atoms, others: [34, 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, 35, 36]) total number of confs: 587 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: REAL250005041901 none CC1=CC1C(=O)NC1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 1, 10, 10, 32, 32, 47, 47, 47, 47, 47, 1, 53, 53, 53, 53, 53, 6, 1, 1, 1, 1, 10, 10, 10, 47, 1, 1] 201 rigid atoms, others: [35, 36, 6, 7, 8, 9, 10, 20, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34]) total number of confs: 222 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041901 none CC1=CC1C(=O)NC1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 13, 13, 13, 53, 53, 53, 145, 145, 199, 199, 201, 201, 201, 201, 201, 53, 2, 2, 2, 1, 1, 13, 53, 53, 53, 53, 145, 145, 145, 201, 53, 53] 201 rigid atoms, others: [0, 1, 2, 3, 4, 24, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 585 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041901 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041901 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041901/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041901 Building REAL250005041902 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041902' /scratch/stefan/7921153/working/building/REAL250005041902 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041902 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041902/0 /scratch/stefan/7921153/working/building/REAL250005041902 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 11) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/11 `/scratch/stefan/7921153/working/3D/11' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(=O)NC1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005041902.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041902.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041902/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041902 none C=CC(=O)NC1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 106 conformations in input total number of sets (complete confs): 106 using faster count positions algorithm for large data unique positions, atoms: [106, 106, 106, 106, 61, 61, 61, 32, 10, 32, 1, 10, 1, 1, 1, 1, 1, 1, 61, 106, 106, 106, 106, 61, 61, 61, 61, 32, 32, 32, 1, 61, 61] 106 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32]) total number of confs: 317 number of broken/clashed sets: 25 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041902 none C=CC(=O)NC1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 106 conformations in input total number of sets (complete confs): 106 using faster count positions algorithm for large data unique positions, atoms: [24, 6, 6, 6, 1, 1, 1, 1, 1, 8, 8, 28, 28, 61, 61, 61, 61, 61, 1, 24, 24, 24, 6, 1, 1, 1, 1, 8, 8, 8, 61, 1, 1] 106 rigid atoms, others: [32, 4, 5, 6, 7, 8, 18, 23, 24, 25, 26, 31] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 27, 28, 29, 30]) total number of confs: 171 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041902 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041902 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041902/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041902 Building REAL250005041903 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041903' /scratch/stefan/7921153/working/building/REAL250005041903 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041903 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041903/0 /scratch/stefan/7921153/working/building/REAL250005041903 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 12) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/12 `/scratch/stefan/7921153/working/3D/12' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC1(C2CCN(C(=O)C3=CC(=O)[N-]O3)CC2)CC1) `REAL250005041903.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041903.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041903/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041903 none CC(=O)NC1(C2CCN(C(=O)C3=CC(=O)[N-]O3)CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 45, 27, 27, 27, 27, 12, 1, 12, 1, 1, 1, 1, 1, 1, 27, 27, 45, 45, 45, 45, 45, 45, 27, 27, 27, 27, 27, 1, 27, 27, 27, 27, 45, 45, 45, 45] 45 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 103 number of broken/clashed sets: 4 ./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: REAL250005041903 none CC(=O)NC1(C2CCN(C(=O)C3=CC(=O)[N-]O3)CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 27, 27, 27, 27, 27, 1, 1, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 27, 1, 1, 1, 1, 8, 8, 8, 8] 45 rigid atoms, others: [32, 33, 34, 4, 5, 6, 7, 8, 9, 17, 18, 25, 26, 27, 28, 29, 31] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 30, 35, 36, 37, 38]) total number of confs: 57 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041903 none CC(=O)NC1(C2CCN(C(=O)C3=CC(=O)[N-]O3)CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [2, 2, 2, 1, 1, 1, 8, 8, 8, 8, 34, 34, 45, 45, 45, 45, 45, 8, 8, 1, 1, 2, 2, 2, 2, 8, 8, 8, 8, 8, 45, 8, 8, 8, 8, 1, 1, 1, 1] 45 rigid atoms, others: [35, 3, 4, 5, 38, 19, 20, 36, 37] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 107 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041903 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041903 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041903/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041903 Building REAL250005041904 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041904' /scratch/stefan/7921153/working/building/REAL250005041904 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041904 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041904/0 /scratch/stefan/7921153/working/building/REAL250005041904 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 13) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/13 `/scratch/stefan/7921153/working/3D/13' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCC(C2(NC(=O)C3=CC(=O)[N-]O3)CC2)CC1) `REAL250005041904.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041904/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041904 none CC(=O)N1CCC(C2(NC(=O)C3=CC(=O)[N-]O3)CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [32, 24, 32, 24, 24, 24, 13, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 13, 13, 24, 24, 32, 32, 32, 24, 24, 24, 24, 24, 6, 1, 13, 13, 13, 13, 24, 24, 24, 24] 32 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 109 number of broken/clashed sets: 19 ./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: REAL250005041904 none CC(=O)N1CCC(C2(NC(=O)C3=CC(=O)[N-]O3)CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [25, 9, 25, 9, 9, 9, 1, 1, 1, 3, 3, 3, 13, 13, 13, 13, 13, 1, 1, 9, 9, 25, 25, 25, 9, 9, 9, 9, 9, 3, 13, 1, 1, 1, 1, 9, 9, 9, 9] 32 rigid atoms, others: [32, 33, 34, 6, 7, 8, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38]) total number of confs: 85 number of broken/clashed sets: 19 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041904 none CC(=O)N1CCC(C2(NC(=O)C3=CC(=O)[N-]O3)CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 1, 1, 1, 1, 1, 9, 10, 10, 10, 24, 24, 24, 24, 24, 9, 9, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 10, 24, 9, 9, 9, 9, 1, 1, 1, 1] 32 rigid atoms, others: [1, 3, 4, 5, 6, 7, 38, 36, 19, 20, 24, 25, 26, 27, 28, 37, 35] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 29, 30, 31, 32, 33, 34]) total number of confs: 55 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041904 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041904 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041904/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041904 Building REAL250005041905 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041905' /scratch/stefan/7921153/working/building/REAL250005041905 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041905 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041905/0 /scratch/stefan/7921153/working/building/REAL250005041905 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 14) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/14 `/scratch/stefan/7921153/working/3D/14' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N(C)CCOCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005041905.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041905.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041905/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041905 none CCC(=O)N(C)CCOCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 195, 161, 195, 101, 161, 101, 35, 11, 8, 1, 2, 1, 2, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 161, 161, 161, 101, 101, 101, 101, 11, 11, 8, 8, 2, 1] 201 rigid atoms, others: [37, 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: 752 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041905 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041905 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041905/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041905 Building REAL250005041906 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041906' /scratch/stefan/7921153/working/building/REAL250005041906 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041906 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041906/0 /scratch/stefan/7921153/working/building/REAL250005041906 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 15) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/15 `/scratch/stefan/7921153/working/3D/15' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N(C)CCOCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005041906.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041906/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041906 none CC(=O)N(C)CCOCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 184, 201, 137, 184, 115, 61, 28, 21, 4, 5, 1, 5, 1, 1, 1, 1, 1, 1, 201, 201, 201, 184, 184, 184, 137, 137, 115, 115, 28, 28, 21, 21, 5, 1] 201 rigid atoms, others: [34, 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: 790 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041906 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041906 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041906/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041906 Building REAL250005041907 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041907' /scratch/stefan/7921153/working/building/REAL250005041907 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041907 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041907/0 /scratch/stefan/7921153/working/building/REAL250005041907 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 16) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/16 `/scratch/stefan/7921153/working/3D/16' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCOCCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CC1) `REAL250005041907.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041907/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041907 none CN(CCOCCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 7, 11, 21, 21, 63, 135, 165, 201, 201, 201, 201, 201, 201, 201, 201, 1, 7, 1, 1, 1, 11, 11, 11, 21, 21, 21, 21, 135, 135, 165, 165, 201, 201, 1, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 38, 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]) total number of confs: 779 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041907 none CN(CCOCCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [123, 79, 79, 33, 11, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 123, 143, 143, 201, 201, 123, 123, 123, 79, 79, 79, 79, 11, 11, 8, 8, 2, 1, 201, 201, 201, 201, 201] 201 rigid atoms, others: [33, 8, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38]) total number of confs: 750 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041907 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041907 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041907/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041907 Building REAL250005041908 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041908' /scratch/stefan/7921153/working/building/REAL250005041908 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041908 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041908/0 /scratch/stefan/7921153/working/building/REAL250005041908 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 17) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/17 `/scratch/stefan/7921153/working/3D/17' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(=O)N(C)CCOCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005041908.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041908.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041908/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041908 none CCCC(=O)N(C)CCOCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 51, 51, 51, 45, 51, 45, 29, 19, 14, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 65, 65, 65, 65, 65, 65, 65, 51, 51, 51, 45, 45, 45, 45, 19, 19, 14, 14, 4, 1] 65 rigid atoms, others: [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, 36, 37, 38, 39]) total number of confs: 292 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041908 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041908 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041908/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041908 Building REAL250005041909 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041909' /scratch/stefan/7921153/working/building/REAL250005041909 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041909 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041909/0 /scratch/stefan/7921153/working/building/REAL250005041909 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 18) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/18 `/scratch/stefan/7921153/working/3D/18' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N(C)CCOCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005041909.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041909.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041909/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041909 none CC(C)C(=O)N(C)CCOCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 159, 201, 110, 159, 106, 39, 15, 12, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 159, 159, 159, 110, 110, 106, 106, 15, 15, 12, 12, 4, 1] 201 rigid atoms, others: [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, 36, 37, 38, 39]) total number of confs: 735 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041909 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041909 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041909/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041909 Building REAL250005041910 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041910' /scratch/stefan/7921153/working/building/REAL250005041910 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041910 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041910/0 /scratch/stefan/7921153/working/building/REAL250005041910 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 19) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/19 `/scratch/stefan/7921153/working/3D/19' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC(=O)N(C)CCOCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005041910.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041910/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041910 none C=CCC(=O)N(C)CCOCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 5, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 31, 31, 31, 28, 31, 28, 26, 14, 11, 2, 3, 1, 3, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 40, 31, 31, 31, 28, 28, 28, 28, 14, 14, 11, 11, 3, 1] 40 rigid atoms, others: [38, 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]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041910 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041910 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041910/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041910 Building REAL250005041911 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041911' /scratch/stefan/7921153/working/building/REAL250005041911 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041911 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041911/0 /scratch/stefan/7921153/working/building/REAL250005041911 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 20) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/20 `/scratch/stefan/7921153/working/3D/20' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCOCCNC(=O)C1=CC(=O)[N-]O1)C(=O)CO) `REAL250005041911.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041911/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041911 none CN(CCOCCNC(=O)C1=CC(=O)[N-]O1)C(=O)CO NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [162, 86, 86, 36, 12, 10, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 162, 195, 195, 201, 162, 162, 162, 86, 86, 86, 86, 12, 12, 10, 10, 4, 1, 201, 201, 603] 603 rigid atoms, others: [32, 8, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35]) total number of confs: 1299 number of broken/clashed sets: 95 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041911 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041911 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041911/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041911 Building REAL250005041912 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041912' /scratch/stefan/7921153/working/building/REAL250005041912 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041912 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041912/0 /scratch/stefan/7921153/working/building/REAL250005041912 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 21) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/21 `/scratch/stefan/7921153/working/3D/21' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=CC(=O)N(C)CCOCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005041912.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041912/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041912 none CC=CC(=O)N(C)CCOCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 61, 67, 59, 61, 53, 47, 29, 20, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 67, 67, 67, 67, 67, 61, 61, 61, 59, 59, 53, 53, 29, 29, 20, 20, 4, 1] 67 rigid atoms, others: [38, 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]) total number of confs: 258 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041912 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041912 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041912/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041912 Building REAL250005041913 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041913' /scratch/stefan/7921153/working/building/REAL250005041913 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041913 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041913/0 /scratch/stefan/7921153/working/building/REAL250005041913 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 22) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/22 `/scratch/stefan/7921153/working/3D/22' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(=O)NCCOCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005041913.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041913.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041913/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041913 none CCCC(=O)NCCOCCN(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 12, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 131, 131, 131, 100, 76, 49, 31, 31, 19, 8, 19, 1, 8, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 131, 100, 100, 76, 76, 31, 31, 31, 31, 19, 19, 19, 1] 201 rigid atoms, others: [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, 36, 37, 38, 39]) total number of confs: 923 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041913 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041913 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041913/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041913 Building REAL250005041914 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041914' /scratch/stefan/7921153/working/building/REAL250005041914 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041914 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041914/0 /scratch/stefan/7921153/working/building/REAL250005041914 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 23) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/23 `/scratch/stefan/7921153/working/3D/23' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)NCCOCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005041914.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041914.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041914/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041914 none CC(C)C(=O)NCCOCCN(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 12, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 170 conformations in input total number of sets (complete confs): 170 using faster count positions algorithm for large data unique positions, atoms: [170, 147, 170, 147, 147, 112, 108, 53, 26, 27, 17, 8, 17, 1, 8, 1, 1, 1, 1, 1, 1, 170, 170, 170, 170, 170, 170, 170, 147, 112, 112, 108, 108, 27, 27, 27, 27, 17, 17, 17, 1] 170 rigid atoms, others: [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, 36, 37, 38, 39]) total number of confs: 698 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041914 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041914 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041914/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041914 Building REAL250005041915 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041915' /scratch/stefan/7921153/working/building/REAL250005041915 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041915 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041915/0 /scratch/stefan/7921153/working/building/REAL250005041915 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 24) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/24 `/scratch/stefan/7921153/working/3D/24' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)NCCOCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005041915.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041915/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041915 none CCC(=O)NCCOCCN(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 12, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 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, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 166 conformations in input total number of sets (complete confs): 166 using faster count positions algorithm for large data unique positions, atoms: [166, 115, 115, 115, 99, 97, 54, 26, 26, 16, 8, 16, 1, 8, 1, 1, 1, 1, 1, 1, 166, 166, 166, 166, 166, 115, 99, 99, 97, 97, 26, 26, 26, 26, 16, 16, 16, 1] 166 rigid atoms, others: [37, 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: 743 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041915 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041915 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041915/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041915 Building REAL250005041916 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041916' /scratch/stefan/7921153/working/building/REAL250005041916 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041916 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041916/0 /scratch/stefan/7921153/working/building/REAL250005041916 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 25) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/25 `/scratch/stefan/7921153/working/3D/25' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCCOCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005041916.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041916/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041916 none CC(=O)NCCOCCN(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 12, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 113, 103, 72, 44, 38, 14, 6, 14, 1, 6, 1, 1, 1, 1, 1, 1, 114, 114, 114, 114, 113, 113, 103, 103, 44, 44, 38, 38, 14, 14, 14, 1] 114 rigid atoms, others: [34, 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: 446 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041916 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041916 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041916/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041916 Building REAL250005041917 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041917' /scratch/stefan/7921153/working/building/REAL250005041917 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041917 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041917/0 /scratch/stefan/7921153/working/building/REAL250005041917 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 26) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/26 `/scratch/stefan/7921153/working/3D/26' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCOCCNC(=O)C1CC1)C(=O)C1=CC(=O)[N-]O1) `REAL250005041917.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041917.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041917/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041917 none CN(CCOCCNC(=O)C1CC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 12, 5, 5, 8, 1, 11, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 196 conformations in input total number of sets (complete confs): 196 using faster count positions algorithm for large data unique positions, atoms: [13, 6, 13, 21, 21, 41, 73, 75, 87, 87, 87, 196, 196, 1, 6, 1, 1, 1, 1, 1, 1, 13, 13, 13, 21, 21, 21, 21, 73, 73, 75, 75, 87, 196, 196, 196, 196, 196, 1] 196 rigid atoms, others: [38, 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]) total number of confs: 661 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041917 none CN(CCOCCNC(=O)C1CC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 12, 5, 5, 8, 1, 11, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 197 conformations in input total number of sets (complete confs): 197 using faster count positions algorithm for large data unique positions, atoms: [134, 134, 108, 85, 53, 39, 13, 13, 1, 13, 1, 1, 1, 134, 190, 190, 197, 197, 197, 197, 197, 134, 134, 134, 134, 134, 112, 112, 53, 53, 39, 39, 13, 1, 1, 1, 1, 1, 197] 197 rigid atoms, others: [33, 34, 35, 36, 37, 8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38]) total number of confs: 748 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041917 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041917 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041917/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041917 Building REAL250005041918 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041918' /scratch/stefan/7921153/working/building/REAL250005041918 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041918 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041918/0 /scratch/stefan/7921153/working/building/REAL250005041918 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 27) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/27 `/scratch/stefan/7921153/working/3D/27' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCOCCNC(=O)CO)C(=O)C1=CC(=O)[N-]O1) `REAL250005041918.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041918.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041918/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041918 none CN(CCOCCNC(=O)CO)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 4, 7, 6, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 516 conformations in input total number of sets (complete confs): 516 using faster count positions algorithm for large data unique positions, atoms: [17, 10, 17, 29, 29, 59, 118, 120, 172, 172, 172, 172, 1, 10, 1, 1, 1, 1, 1, 1, 17, 17, 17, 29, 29, 29, 29, 118, 118, 120, 120, 172, 172, 172, 516, 1] 516 rigid atoms, others: [35, 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]) total number of confs: 1120 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041918 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041918 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041918/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041918 Building REAL250005041919 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041919' /scratch/stefan/7921153/working/building/REAL250005041919 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041919 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041919/0 /scratch/stefan/7921153/working/building/REAL250005041919 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 28) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/28 `/scratch/stefan/7921153/working/3D/28' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)C(=O)NCCOCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005041919.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041919.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041919/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041919 none CC(=O)C(=O)NCCOCCN(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 11, 8, 5, 5, 12, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 193, 201, 193, 193, 125, 119, 65, 29, 29, 16, 9, 16, 1, 9, 1, 1, 1, 1, 1, 1, 201, 201, 201, 193, 125, 125, 119, 119, 29, 29, 29, 29, 16, 16, 16, 1] 201 rigid atoms, others: [36, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 711 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041919 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041919 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041919/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041919 Building REAL250005041920 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041920' /scratch/stefan/7921153/working/building/REAL250005041920 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041920 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041920/0 /scratch/stefan/7921153/working/building/REAL250005041920 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 29) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/29 `/scratch/stefan/7921153/working/3D/29' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=CC(=O)NCCOCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005041920.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041920.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041920/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041920 none CC=CC(=O)NCCOCCN(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 12, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 175, 175, 175, 137, 115, 81, 51, 33, 17, 8, 17, 1, 8, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 175, 137, 137, 115, 115, 51, 51, 33, 33, 17, 17, 17, 1] 201 rigid atoms, others: [38, 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]) total number of confs: 827 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041920 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041920 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041920/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041920 Building REAL250005041921 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041921' /scratch/stefan/7921153/working/building/REAL250005041921 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041921 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041921/0 /scratch/stefan/7921153/working/building/REAL250005041921 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 30) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/30 `/scratch/stefan/7921153/working/3D/30' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC(=O)NCCOCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005041921.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041921.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041921/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041921 none C=CCC(=O)NCCOCCN(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 12, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 136, 136, 136, 96, 73, 45, 29, 29, 19, 8, 19, 1, 8, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 136, 96, 96, 73, 73, 29, 29, 29, 29, 19, 19, 19, 1] 201 rigid atoms, others: [38, 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]) total number of confs: 921 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041921 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041921 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041921/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041921 Building REAL250005041922 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041922' /scratch/stefan/7921153/working/building/REAL250005041922 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041922 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041922/0 /scratch/stefan/7921153/working/building/REAL250005041922 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 31) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/31 `/scratch/stefan/7921153/working/3D/31' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCOCCNC(=O)CC#N)C(=O)C1=CC(=O)[N-]O1) `REAL250005041922.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041922.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041922/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041922 none CN(CCOCCNC(=O)CC#N)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.1', 'N.1', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 12, 5, 5, 8, 1, 11, 5, 1, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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: [11, 6, 11, 19, 19, 36, 68, 68, 88, 88, 88, 152, 152, 1, 6, 1, 1, 1, 1, 1, 1, 11, 11, 11, 19, 19, 19, 19, 68, 68, 68, 68, 88, 152, 152, 1] 152 rigid atoms, others: [35, 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]) total number of confs: 627 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041922 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041922 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041922/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041922 Building REAL250005041923 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041923' /scratch/stefan/7921153/working/building/REAL250005041923 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041923 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041923/0 /scratch/stefan/7921153/working/building/REAL250005041923 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 32) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/32 `/scratch/stefan/7921153/working/3D/32' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(=O)NCCOCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005041923.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041923.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041923/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041923 none C=CC(=O)NCCOCCN(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 12, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 104 conformations in input total number of sets (complete confs): 104 using faster count positions algorithm for large data unique positions, atoms: [104, 104, 104, 104, 87, 83, 51, 25, 27, 15, 8, 15, 1, 8, 1, 1, 1, 1, 1, 1, 104, 104, 104, 104, 87, 87, 83, 83, 27, 27, 27, 27, 15, 15, 15, 1] 104 rigid atoms, others: [35, 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]) total number of confs: 411 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041923 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041923 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041923/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041923 Building REAL250005041924 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041924' /scratch/stefan/7921153/working/building/REAL250005041924 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041924 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041924/0 /scratch/stefan/7921153/working/building/REAL250005041924 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 33) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/33 `/scratch/stefan/7921153/working/3D/33' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)NCC1=CCN(C(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005041924.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041924/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041924 none CCC(=O)NCC1=CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 160, 160, 160, 87, 20, 20, 20, 20, 8, 1, 8, 1, 1, 1, 1, 1, 1, 20, 20, 201, 201, 201, 201, 201, 160, 87, 87, 20, 20, 20, 1, 20, 20, 20, 20] 201 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35]) total number of confs: 765 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041924 none CCC(=O)NCC1=CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [122, 48, 48, 48, 10, 1, 1, 1, 1, 1, 1, 7, 7, 20, 20, 20, 20, 20, 1, 1, 122, 122, 122, 122, 122, 48, 10, 10, 1, 1, 1, 20, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 10, 18, 19, 28, 29, 30] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 476 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041924 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041924 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041924/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041924 Building REAL250005041925 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041925' /scratch/stefan/7921153/working/building/REAL250005041925 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041925 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041925/0 /scratch/stefan/7921153/working/building/REAL250005041925 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 34) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/34 `/scratch/stefan/7921153/working/3D/34' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC1=CCN(C(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005041925.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041925/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041925 none CC(=O)NCC1=CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 116, 33, 33, 33, 33, 11, 1, 11, 1, 1, 1, 1, 1, 1, 33, 33, 140, 140, 140, 140, 116, 116, 33, 33, 33, 1, 33, 33, 33, 33] 140 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32]) total number of confs: 477 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041925 none CC(=O)NCC1=CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 140 conformations in input total number of sets (complete confs): 140 using faster count positions algorithm for large data unique positions, atoms: [54, 54, 54, 13, 1, 1, 1, 1, 1, 1, 7, 7, 33, 33, 33, 33, 33, 1, 1, 54, 54, 54, 54, 13, 13, 1, 1, 1, 33, 1, 1, 1, 1] 140 rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 17, 18, 25, 26, 27, 29, 30, 31] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 28]) total number of confs: 190 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041925 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041925 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041925/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041925 Building REAL250005041926 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041926' /scratch/stefan/7921153/working/building/REAL250005041926 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041926 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041926/0 /scratch/stefan/7921153/working/building/REAL250005041926 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 35) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/35 `/scratch/stefan/7921153/working/3D/35' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1=CCN(C(=O)C2=CC(=O)[N-]O2)CC1)C1CC1) `REAL250005041926.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041926/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041926 none O=C(NCC1=CCN(C(=O)C2=CC(=O)[N-]O2)CC1)C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 51, 116, 116, 116, 116, 193, 193, 201, 201, 201, 201, 201, 116, 116, 1, 1, 1, 11, 51, 51, 116, 116, 116, 201, 116, 116, 116, 116, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 1, 34, 35, 36, 33, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 516 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: REAL250005041926 none O=C(NCC1=CCN(C(=O)C2=CC(=O)[N-]O2)CC1)C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 71, 15, 15, 15, 15, 7, 1, 7, 1, 1, 1, 1, 1, 1, 15, 15, 124, 201, 201, 124, 71, 71, 15, 15, 15, 1, 15, 15, 15, 15, 201, 201, 201, 201, 201] 201 rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 660 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041926 none O=C(NCC1=CCN(C(=O)C2=CC(=O)[N-]O2)CC1)C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 1, 1, 1, 1, 1, 1, 7, 7, 15, 15, 15, 15, 15, 1, 1, 43, 116, 116, 43, 10, 10, 1, 1, 1, 15, 1, 1, 1, 1, 116, 116, 116, 116, 116] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 16, 17, 24, 25, 26, 28, 29, 30, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 27, 32, 33, 34, 35, 36]) total number of confs: 352 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041926 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041926 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041926/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041926 Building REAL250005041927 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041927' /scratch/stefan/7921153/working/building/REAL250005041927 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041927 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041927/0 /scratch/stefan/7921153/working/building/REAL250005041927 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 36) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/36 `/scratch/stefan/7921153/working/3D/36' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)NCC1=CCN(C(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005041927.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041927.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041927/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041927 none COCC(=O)NCC1=CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 151, 151, 151, 61, 13, 13, 13, 13, 6, 1, 6, 1, 1, 1, 1, 1, 1, 13, 13, 201, 201, 201, 201, 201, 151, 61, 61, 13, 13, 13, 1, 13, 13, 13, 13] 201 rigid atoms, others: [32, 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, 33, 34, 35, 36]) total number of confs: 746 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041927 none COCC(=O)NCC1=CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [112, 99, 39, 39, 39, 9, 1, 1, 1, 1, 1, 1, 7, 7, 13, 13, 13, 13, 13, 1, 1, 112, 112, 112, 101, 101, 39, 9, 9, 1, 1, 1, 13, 1, 1, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 6, 7, 8, 9, 10, 11, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 32]) total number of confs: 428 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041927 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041927 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041927/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041927 Building REAL250005041928 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041928' /scratch/stefan/7921153/working/building/REAL250005041928 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041928 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041928/0 /scratch/stefan/7921153/working/building/REAL250005041928 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 37) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/37 `/scratch/stefan/7921153/working/3D/37' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(=O)NCC1=CCN(C(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005041928.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041928/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041928 none CCCC(=O)NCC1=CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 200, 123, 123, 123, 54, 12, 12, 12, 12, 6, 1, 6, 1, 1, 1, 1, 1, 1, 12, 12, 201, 201, 201, 201, 201, 200, 200, 123, 54, 54, 12, 12, 12, 1, 12, 12, 12, 12] 201 rigid atoms, others: [34, 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, 35, 36, 37, 38]) total number of confs: 805 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041928 none CCCC(=O)NCC1=CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 118, 35, 35, 35, 8, 1, 1, 1, 1, 1, 1, 7, 7, 12, 12, 12, 12, 12, 1, 1, 136, 136, 136, 136, 136, 118, 118, 35, 8, 8, 1, 1, 1, 12, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 35, 36, 37, 6, 7, 8, 9, 10, 11, 19, 20, 38, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34]) total number of confs: 595 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041928 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041928 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041928/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041928 Building REAL250005041929 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041929' /scratch/stefan/7921153/working/building/REAL250005041929 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041929 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041929/0 /scratch/stefan/7921153/working/building/REAL250005041929 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 38) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/38 `/scratch/stefan/7921153/working/3D/38' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)NCC1=CCN(C(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005041929.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041929.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041929/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041929 none CC(C)C(=O)NCC1=CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 173, 201, 173, 173, 85, 18, 18, 18, 18, 8, 1, 8, 1, 1, 1, 1, 1, 1, 18, 18, 201, 201, 201, 201, 201, 201, 201, 173, 85, 85, 18, 18, 18, 1, 18, 18, 18, 18] 201 rigid atoms, others: [34, 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, 35, 36, 37, 38]) total number of confs: 724 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041929 none CC(C)C(=O)NCC1=CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 45, 113, 45, 45, 10, 1, 1, 1, 1, 1, 1, 7, 7, 18, 18, 18, 18, 18, 1, 1, 113, 113, 113, 113, 113, 113, 113, 45, 10, 10, 1, 1, 1, 18, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 35, 36, 37, 6, 7, 8, 9, 10, 11, 19, 20, 38, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34]) total number of confs: 454 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041929 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041929 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041929/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041929 Building REAL250005041930 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041930' /scratch/stefan/7921153/working/building/REAL250005041930 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041930 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041930/0 /scratch/stefan/7921153/working/building/REAL250005041930 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 39) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/39 `/scratch/stefan/7921153/working/3D/39' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C(=O)NCC1=CCN(C(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005041930.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041930.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041930/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041930 none NC(=O)C(=O)NCC1=CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 200, 201, 200, 200, 122, 26, 26, 26, 26, 9, 1, 9, 1, 1, 1, 1, 1, 1, 26, 26, 201, 201, 200, 122, 122, 26, 26, 26, 1, 26, 26, 26, 26] 201 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33]) total number of confs: 655 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041930 none NC(=O)C(=O)NCC1=CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [74, 52, 74, 52, 52, 12, 1, 1, 1, 1, 1, 1, 7, 7, 26, 26, 26, 26, 26, 1, 1, 74, 74, 52, 12, 12, 1, 1, 1, 26, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 19, 20, 26, 27, 28, 30, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 29]) total number of confs: 260 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041930 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041930 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041930/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041930 Building REAL250005041931 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041931' /scratch/stefan/7921153/working/building/REAL250005041931 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041931 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041931/0 /scratch/stefan/7921153/working/building/REAL250005041931 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 40) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/40 `/scratch/stefan/7921153/working/3D/40' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC(=O)NCC1=CCN(C(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005041931.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041931.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041931/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041931 none C=CCC(=O)NCC1=CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 139, 139, 139, 65, 15, 15, 15, 15, 7, 1, 7, 1, 1, 1, 1, 1, 1, 15, 15, 201, 201, 201, 201, 201, 139, 65, 65, 15, 15, 15, 1, 15, 15, 15, 15] 201 rigid atoms, others: [32, 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, 33, 34, 35, 36]) total number of confs: 765 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041931 none C=CCC(=O)NCC1=CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [132, 112, 35, 35, 35, 7, 1, 1, 1, 1, 1, 1, 7, 7, 15, 15, 15, 15, 15, 1, 1, 132, 132, 132, 112, 112, 35, 7, 7, 1, 1, 1, 15, 1, 1, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 6, 7, 8, 9, 10, 11, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 32]) total number of confs: 501 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041931 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041931 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041931/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041931 Building REAL250005041932 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041932' /scratch/stefan/7921153/working/building/REAL250005041932 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041932 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041932/0 /scratch/stefan/7921153/working/building/REAL250005041932 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 41) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/41 `/scratch/stefan/7921153/working/3D/41' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CO)NCC1=CCN(C(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005041932.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041932/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041932 none O=C(CO)NCC1=CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [199, 199, 199, 201, 125, 30, 30, 30, 30, 10, 1, 10, 1, 1, 1, 1, 1, 1, 30, 30, 201, 201, 603, 199, 125, 125, 30, 30, 30, 1, 30, 30, 30, 30] 603 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33]) total number of confs: 1276 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041932 none O=C(CO)NCC1=CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [54, 54, 54, 107, 12, 1, 1, 1, 1, 1, 1, 7, 7, 30, 30, 30, 30, 30, 1, 1, 109, 109, 327, 54, 12, 12, 1, 1, 1, 30, 1, 1, 1, 1] 603 rigid atoms, others: [32, 33, 5, 6, 7, 8, 9, 10, 18, 19, 26, 27, 28, 30, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 29]) total number of confs: 783 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041932 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041932 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041932/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041932 Building REAL250005041933 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041933' /scratch/stefan/7921153/working/building/REAL250005041933 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041933 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041933/0 /scratch/stefan/7921153/working/building/REAL250005041933 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 42) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/42 `/scratch/stefan/7921153/working/3D/42' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)C(=O)NCC1=CCN(C(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005041933.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041933/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041933 none CC(O)C(=O)NCC1=CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [201, 190, 201, 190, 190, 94, 20, 20, 20, 20, 8, 1, 8, 1, 1, 1, 1, 1, 1, 20, 20, 201, 201, 201, 201, 603, 190, 94, 94, 20, 20, 20, 1, 20, 20, 20, 20] 603 rigid atoms, others: [32, 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, 33, 34, 35, 36]) total number of confs: 1268 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041933 none CC(O)C(=O)NCC1=CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [116, 52, 116, 52, 52, 12, 1, 1, 1, 1, 1, 1, 7, 7, 20, 20, 20, 20, 20, 1, 1, 116, 116, 116, 116, 348, 52, 12, 12, 1, 1, 1, 20, 1, 1, 1, 1] 603 rigid atoms, others: [33, 34, 35, 36, 6, 7, 8, 9, 10, 11, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 32]) total number of confs: 800 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041933 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041933 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041933/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041933 Building REAL250005041934 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041934' /scratch/stefan/7921153/working/building/REAL250005041934 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041934 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041934/0 /scratch/stefan/7921153/working/building/REAL250005041934 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 43) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/43 `/scratch/stefan/7921153/working/3D/43' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCF)NCC1=CCN(C(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005041934.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041934.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041934/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041934 none O=C(CCF)NCC1=CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'F', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 15, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 201, 201, 57, 13, 13, 13, 13, 6, 1, 6, 1, 1, 1, 1, 1, 1, 13, 13, 201, 201, 201, 201, 118, 57, 57, 13, 13, 13, 1, 13, 13, 13, 13] 201 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 31] 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, 32, 33, 34, 35]) total number of confs: 780 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041934 none O=C(CCF)NCC1=CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'F', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 15, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 33, 125, 136, 8, 1, 1, 1, 1, 1, 1, 7, 7, 13, 13, 13, 13, 13, 1, 1, 125, 125, 136, 136, 33, 8, 8, 1, 1, 1, 13, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 6, 7, 8, 9, 10, 11, 19, 20, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 536 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041934 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041934 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041934/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041934 Building REAL250005041935 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041935' /scratch/stefan/7921153/working/building/REAL250005041935 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041935 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041935/0 /scratch/stefan/7921153/working/building/REAL250005041935 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 44) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/44 `/scratch/stefan/7921153/working/3D/44' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](O)C(=O)NCC1=CCN(C(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005041935.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041935/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041935 none C[C@@H](O)C(=O)NCC1=CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [201, 189, 201, 200, 189, 189, 94, 19, 19, 19, 19, 8, 1, 8, 1, 1, 1, 1, 1, 1, 19, 19, 201, 201, 201, 603, 189, 94, 94, 19, 19, 19, 1, 19, 19, 19, 19] 603 rigid atoms, others: [32, 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, 33, 34, 35, 36]) total number of confs: 1275 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041935 none C[C@@H](O)C(=O)NCC1=CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [116, 52, 116, 115, 52, 52, 12, 1, 1, 1, 1, 1, 1, 7, 7, 19, 19, 19, 19, 19, 1, 1, 116, 116, 116, 348, 52, 12, 12, 1, 1, 1, 19, 1, 1, 1, 1] 603 rigid atoms, others: [33, 34, 35, 36, 7, 8, 9, 10, 11, 12, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 32]) total number of confs: 798 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041935 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041935 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041935/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041935 Building REAL250005041936 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041936' /scratch/stefan/7921153/working/building/REAL250005041936 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041936 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041936/0 /scratch/stefan/7921153/working/building/REAL250005041936 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 45) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/45 `/scratch/stefan/7921153/working/3D/45' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](O)C(=O)NCC1=CCN(C(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005041936.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041936/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041936 none C[C@H](O)C(=O)NCC1=CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [201, 192, 201, 200, 192, 192, 99, 20, 20, 20, 20, 8, 1, 8, 1, 1, 1, 1, 1, 1, 20, 20, 201, 201, 201, 603, 192, 99, 99, 20, 20, 20, 1, 20, 20, 20, 20] 603 rigid atoms, others: [32, 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, 33, 34, 35, 36]) total number of confs: 1286 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041936 none C[C@H](O)C(=O)NCC1=CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [119, 54, 119, 117, 54, 54, 12, 1, 1, 1, 1, 1, 1, 7, 7, 20, 20, 20, 20, 20, 1, 1, 119, 119, 119, 357, 54, 12, 12, 1, 1, 1, 20, 1, 1, 1, 1] 603 rigid atoms, others: [33, 34, 35, 36, 7, 8, 9, 10, 11, 12, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 32]) total number of confs: 827 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041936 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041936 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041936/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041936 Building REAL250005041937 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041937' /scratch/stefan/7921153/working/building/REAL250005041937 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041937 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041937/0 /scratch/stefan/7921153/working/building/REAL250005041937 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 46) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/46 `/scratch/stefan/7921153/working/3D/46' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=CC(=O)NCC1=CCN(C(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005041937.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041937.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041937/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041937 none CC=CC(=O)NCC1=CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 169, 169, 169, 90, 18, 18, 18, 18, 8, 1, 8, 1, 1, 1, 1, 1, 1, 18, 18, 201, 201, 201, 201, 201, 169, 90, 90, 18, 18, 18, 1, 18, 18, 18, 18] 201 rigid atoms, others: [32, 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, 33, 34, 35, 36]) total number of confs: 670 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041937 none CC=CC(=O)NCC1=CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [104, 104, 49, 49, 49, 11, 1, 1, 1, 1, 1, 1, 7, 7, 18, 18, 18, 18, 18, 1, 1, 104, 104, 104, 104, 104, 49, 11, 11, 1, 1, 1, 18, 1, 1, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 6, 7, 8, 9, 10, 11, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 32]) total number of confs: 334 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041937 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041937 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041937/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041937 Building REAL250005041938 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041938' /scratch/stefan/7921153/working/building/REAL250005041938 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041938 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041938/0 /scratch/stefan/7921153/working/building/REAL250005041938 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 47) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/47 `/scratch/stefan/7921153/working/3D/47' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)N1CC=C(CNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005041938.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041938.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041938/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041938 none COCC(=O)N1CC=C(CNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 194, 120, 64, 120, 64, 64, 64, 15, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 64, 64, 201, 201, 201, 194, 194, 64, 64, 64, 14, 14, 4, 1, 64, 64, 64, 64] 201 rigid atoms, others: [32, 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, 33, 34, 35, 36]) total number of confs: 695 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041938 none COCC(=O)N1CC=C(CNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [40, 17, 6, 1, 6, 1, 1, 1, 1, 1, 11, 55, 55, 55, 64, 64, 64, 64, 64, 1, 1, 40, 40, 40, 17, 17, 1, 1, 1, 11, 11, 55, 64, 1, 1, 1, 1] 201 rigid atoms, others: [33, 34, 3, 36, 5, 6, 7, 8, 9, 19, 20, 26, 27, 28, 35] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 29, 30, 31, 32]) total number of confs: 256 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041938 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041938 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041938/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041938 Building REAL250005041939 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041939' /scratch/stefan/7921153/working/building/REAL250005041939 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041939 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041939/0 /scratch/stefan/7921153/working/building/REAL250005041939 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 48) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/48 `/scratch/stefan/7921153/working/3D/48' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(=O)N1CC=C(CNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005041939.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041939/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041939 none CCCC(=O)N1CC=C(CNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 200, 151, 68, 151, 68, 68, 68, 18, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 68, 68, 201, 201, 201, 201, 201, 200, 200, 68, 68, 68, 17, 17, 4, 1, 68, 68, 68, 68] 201 rigid atoms, others: [34, 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, 35, 36, 37, 38]) total number of confs: 619 number of broken/clashed sets: 17 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041939 none CCCC(=O)N1CC=C(CNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 6, 1, 6, 1, 1, 1, 1, 1, 12, 55, 55, 55, 68, 68, 68, 68, 68, 1, 1, 33, 33, 33, 32, 32, 18, 18, 1, 1, 1, 12, 12, 55, 68, 1, 1, 1, 1] 201 rigid atoms, others: [35, 3, 36, 5, 6, 7, 8, 9, 19, 20, 38, 28, 29, 30, 37] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34]) total number of confs: 328 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041939 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041939 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041939/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041939 Building REAL250005041940 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041940' /scratch/stefan/7921153/working/building/REAL250005041940 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041940 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041940/0 /scratch/stefan/7921153/working/building/REAL250005041940 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 49) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/49 `/scratch/stefan/7921153/working/3D/49' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N1CC=C(CNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005041940.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041940.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041940/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041940 none CC(C)C(=O)N1CC=C(CNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 199, 201, 113, 199, 113, 113, 113, 31, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 113, 113, 201, 201, 201, 201, 201, 201, 201, 113, 113, 113, 31, 31, 7, 1, 113, 113, 113, 113] 201 rigid atoms, others: [34, 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, 35, 36, 37, 38]) total number of confs: 479 number of broken/clashed sets: 64 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041940 none CC(C)C(=O)N1CC=C(CNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 18, 1, 7, 1, 1, 1, 1, 1, 13, 74, 74, 74, 113, 113, 113, 113, 113, 1, 1, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 13, 13, 74, 113, 1, 1, 1, 1] 201 rigid atoms, others: [35, 3, 36, 5, 6, 7, 8, 9, 19, 20, 38, 28, 29, 30, 37] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34]) total number of confs: 323 number of broken/clashed sets: 64 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041940 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041940 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041940/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041940 Building REAL250005041941 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041941' /scratch/stefan/7921153/working/building/REAL250005041941 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041941 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041941/0 /scratch/stefan/7921153/working/building/REAL250005041941 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 50) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/50 `/scratch/stefan/7921153/working/3D/50' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N1CC=C(CNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005041941.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041941.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041941/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041941 none CCC(=O)N1CC=C(CNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 191 conformations in input total number of sets (complete confs): 191 using faster count positions algorithm for large data unique positions, atoms: [191, 189, 117, 189, 117, 117, 117, 36, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 117, 117, 191, 191, 191, 191, 191, 117, 117, 117, 35, 35, 9, 1, 117, 117, 117, 117] 191 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35]) total number of confs: 479 number of broken/clashed sets: 31 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041941 none CCC(=O)N1CC=C(CNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 191 conformations in input total number of sets (complete confs): 191 using faster count positions algorithm for large data unique positions, atoms: [21, 6, 1, 6, 1, 1, 1, 1, 1, 13, 74, 74, 74, 117, 117, 117, 117, 117, 1, 1, 22, 22, 22, 21, 21, 1, 1, 1, 13, 13, 74, 117, 1, 1, 1, 1] 191 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 34, 18, 19, 25, 26, 27] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 28, 29, 30, 31]) total number of confs: 346 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041941 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041941 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041941/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041941 Building REAL250005041942 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041942' /scratch/stefan/7921153/working/building/REAL250005041942 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041942 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041942/0 /scratch/stefan/7921153/working/building/REAL250005041942 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 51) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/51 `/scratch/stefan/7921153/working/3D/51' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CC=C(CNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005041942.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041942.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041942/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041942 none CC(=O)N1CC=C(CNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 102 conformations in input total number of sets (complete confs): 102 using faster count positions algorithm for large data unique positions, atoms: [102, 85, 102, 85, 85, 85, 35, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 85, 85, 102, 102, 102, 85, 85, 85, 34, 34, 8, 1, 85, 85, 85, 85] 102 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32]) total number of confs: 255 number of broken/clashed sets: 19 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041942 none CC(=O)N1CC=C(CNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 102 conformations in input total number of sets (complete confs): 102 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 1, 1, 1, 1, 1, 13, 61, 61, 61, 85, 85, 85, 85, 85, 1, 1, 5, 5, 5, 1, 1, 1, 13, 13, 61, 85, 1, 1, 1, 1] 102 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 17, 18, 22, 23, 24, 29, 30, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 25, 26, 27, 28]) total number of confs: 214 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041942 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041942 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041942/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041942 Building REAL250005041943 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041943' /scratch/stefan/7921153/working/building/REAL250005041943 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041943 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041943/0 /scratch/stefan/7921153/working/building/REAL250005041943 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 52) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/52 `/scratch/stefan/7921153/working/3D/52' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1=CCN(C(=O)C2CC2)CC1)C1=CC(=O)[N-]O1) `REAL250005041943.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041943/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041943 none O=C(NCC1=CCN(C(=O)C2CC2)CC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 29, 102, 102, 102, 102, 151, 151, 201, 201, 102, 102, 1, 1, 1, 1, 1, 1, 6, 29, 29, 102, 102, 102, 201, 201, 201, 201, 201, 102, 102, 102, 102, 1] 201 rigid atoms, others: [1, 36, 15, 16, 17, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 571 number of broken/clashed sets: 9 ./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: REAL250005041943 none O=C(NCC1=CCN(C(=O)C2CC2)CC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 111, 23, 23, 23, 23, 8, 1, 8, 1, 1, 1, 23, 23, 194, 201, 201, 201, 201, 201, 194, 111, 111, 23, 23, 23, 1, 1, 1, 1, 1, 23, 23, 23, 23, 201] 201 rigid atoms, others: [8, 10, 11, 12, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 32, 33, 34, 35, 36]) total number of confs: 639 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041943 none O=C(NCC1=CCN(C(=O)C2CC2)CC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 1, 1, 1, 1, 1, 1, 6, 6, 23, 23, 1, 1, 75, 102, 102, 102, 102, 102, 75, 13, 13, 1, 1, 1, 23, 23, 23, 23, 23, 1, 1, 1, 1, 102] 201 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 13, 14, 35, 24, 25, 26] set([0, 1, 2, 9, 10, 11, 12, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 36]) total number of confs: 296 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041943 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041943 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041943/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041943 Building REAL250005041944 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041944' /scratch/stefan/7921153/working/building/REAL250005041944 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041944 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041944/0 /scratch/stefan/7921153/working/building/REAL250005041944 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 53) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/53 `/scratch/stefan/7921153/working/3D/53' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C(=O)N1CC=C(CNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005041944.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041944.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041944/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041944 none NC(=O)C(=O)N1CC=C(CNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 120, 166, 85, 120, 85, 85, 85, 24, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 85, 85, 166, 166, 85, 85, 85, 24, 24, 6, 1, 85, 85, 85, 85] 166 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33]) total number of confs: 468 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041944 none NC(=O)C(=O)N1CC=C(CNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [21, 7, 21, 1, 7, 1, 1, 1, 1, 1, 13, 65, 65, 65, 85, 85, 85, 85, 85, 1, 1, 21, 21, 1, 1, 1, 13, 13, 65, 85, 1, 1, 1, 1] 166 rigid atoms, others: [32, 33, 3, 5, 6, 7, 8, 9, 19, 20, 23, 24, 25, 30, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 26, 27, 28, 29]) total number of confs: 257 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041944 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041944 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041944/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041944 Building REAL250005041945 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041945' /scratch/stefan/7921153/working/building/REAL250005041945 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041945 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041945/0 /scratch/stefan/7921153/working/building/REAL250005041945 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 54) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/54 `/scratch/stefan/7921153/working/3D/54' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CO)N1CC=C(CNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005041945.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041945.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041945/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041945 none O=C(CO)N1CC=C(CNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [195, 125, 195, 201, 125, 125, 125, 33, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 125, 125, 201, 201, 603, 125, 125, 125, 32, 32, 7, 1, 125, 125, 125, 125] 603 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33]) total number of confs: 1115 number of broken/clashed sets: 89 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041945 none O=C(CO)N1CC=C(CNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 26, 1, 1, 1, 1, 1, 13, 77, 77, 77, 125, 125, 125, 125, 125, 1, 1, 26, 26, 78, 1, 1, 1, 13, 13, 77, 125, 1, 1, 1, 1] 603 rigid atoms, others: [32, 1, 4, 5, 6, 7, 8, 18, 19, 23, 24, 25, 33, 30, 31] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 26, 27, 28, 29]) total number of confs: 445 number of broken/clashed sets: 89 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041945 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041945 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041945/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041945 Building REAL250005041946 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041946' /scratch/stefan/7921153/working/building/REAL250005041946 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041946 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041946/0 /scratch/stefan/7921153/working/building/REAL250005041946 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 55) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/55 `/scratch/stefan/7921153/working/3D/55' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)C(=O)N1CC=C(CNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005041946.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041946.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041946/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041946 none CC(O)C(=O)N1CC=C(CNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 459 conformations in input total number of sets (complete confs): 459 using faster count positions algorithm for large data unique positions, atoms: [153, 132, 153, 87, 132, 87, 87, 87, 29, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 87, 87, 153, 153, 153, 153, 459, 87, 87, 87, 28, 28, 6, 1, 87, 87, 87, 87] 459 rigid atoms, others: [32, 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, 33, 34, 35, 36]) total number of confs: 909 number of broken/clashed sets: 92 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041946 none CC(O)C(=O)N1CC=C(CNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 459 conformations in input total number of sets (complete confs): 459 using faster count positions algorithm for large data unique positions, atoms: [21, 7, 21, 1, 7, 1, 1, 1, 1, 1, 13, 66, 66, 66, 87, 87, 87, 87, 87, 1, 1, 21, 21, 21, 21, 63, 1, 1, 1, 13, 13, 66, 87, 1, 1, 1, 1] 459 rigid atoms, others: [33, 34, 3, 36, 5, 6, 7, 8, 9, 19, 20, 26, 27, 28, 35] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 29, 30, 31, 32]) total number of confs: 345 number of broken/clashed sets: 92 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041946 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041946 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041946/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041946 Building REAL250005041947 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041947' /scratch/stefan/7921153/working/building/REAL250005041947 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041947 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041947/0 /scratch/stefan/7921153/working/building/REAL250005041947 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 56) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/56 `/scratch/stefan/7921153/working/3D/56' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)C(=O)N1CC=C(CNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005041947.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041947.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041947/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041947 none CC(=O)C(=O)N1CC=C(CNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 161, 201, 103, 161, 103, 103, 103, 28, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 103, 103, 201, 201, 201, 103, 103, 103, 27, 27, 7, 1, 103, 103, 103, 103] 201 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34]) total number of confs: 550 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041947 none CC(=O)C(=O)N1CC=C(CNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [24, 7, 24, 1, 7, 1, 1, 1, 1, 1, 13, 68, 68, 68, 103, 103, 103, 103, 103, 1, 1, 24, 24, 24, 1, 1, 1, 13, 13, 68, 103, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 3, 5, 6, 7, 8, 9, 19, 20, 24, 25, 26, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 27, 28, 29, 30]) total number of confs: 303 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041947 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041947 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041947/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041947 Building REAL250005041948 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041948' /scratch/stefan/7921153/working/building/REAL250005041948 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041948 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041948/0 /scratch/stefan/7921153/working/building/REAL250005041948 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 57) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/57 `/scratch/stefan/7921153/working/3D/57' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=CC(=O)N1CC=C(CNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005041948.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041948/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041948 none CC=CC(=O)N1CC=C(CNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 197 conformations in input total number of sets (complete confs): 197 using faster count positions algorithm for large data unique positions, atoms: [197, 197, 178, 101, 178, 101, 101, 101, 28, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 101, 101, 197, 197, 197, 197, 197, 101, 101, 101, 27, 27, 7, 1, 101, 101, 101, 101] 197 rigid atoms, others: [32, 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, 33, 34, 35, 36]) total number of confs: 508 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041948 none CC=CC(=O)N1CC=C(CNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 197 conformations in input total number of sets (complete confs): 197 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 6, 1, 6, 1, 1, 1, 1, 1, 13, 68, 68, 68, 101, 101, 101, 101, 101, 1, 1, 33, 33, 33, 33, 33, 1, 1, 1, 13, 13, 68, 101, 1, 1, 1, 1] 197 rigid atoms, others: [33, 34, 3, 36, 5, 6, 7, 8, 9, 19, 20, 26, 27, 28, 35] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 29, 30, 31, 32]) total number of confs: 314 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041948 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041948 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041948/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041948 Building REAL250005041949 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041949' /scratch/stefan/7921153/working/building/REAL250005041949 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041949 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041949/0 /scratch/stefan/7921153/working/building/REAL250005041949 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 58) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/58 `/scratch/stefan/7921153/working/3D/58' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](O)C(=O)N1CC=C(CNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005041949.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041949.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041949/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041949 none C[C@H](O)C(=O)N1CC=C(CNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [201, 175, 201, 201, 95, 175, 95, 95, 95, 33, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 95, 95, 201, 201, 201, 603, 95, 95, 95, 32, 32, 8, 1, 95, 95, 95, 95] 603 rigid atoms, others: [32, 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, 33, 34, 35, 36]) total number of confs: 1195 number of broken/clashed sets: 198 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041949 none C[C@H](O)C(=O)N1CC=C(CNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [23, 6, 23, 23, 1, 6, 1, 1, 1, 1, 1, 13, 69, 69, 69, 95, 95, 95, 95, 95, 1, 1, 23, 23, 23, 69, 1, 1, 1, 13, 13, 69, 95, 1, 1, 1, 1] 603 rigid atoms, others: [33, 34, 35, 4, 6, 7, 8, 9, 10, 20, 21, 36, 26, 27, 28] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 29, 30, 31, 32]) total number of confs: 372 number of broken/clashed sets: 198 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041949 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041949 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041949/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041949 Building REAL250005041950 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041950' /scratch/stefan/7921153/working/building/REAL250005041950 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041950 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041950/0 /scratch/stefan/7921153/working/building/REAL250005041950 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 59) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/59 `/scratch/stefan/7921153/working/3D/59' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC(=O)N1CC=C(CNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005041950.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041950.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041950/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041950 none C=CCC(=O)N1CC=C(CNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 142, 61, 142, 61, 61, 61, 14, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 61, 61, 201, 201, 201, 201, 201, 61, 61, 61, 13, 13, 4, 1, 61, 61, 61, 61] 201 rigid atoms, others: [32, 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, 33, 34, 35, 36]) total number of confs: 670 number of broken/clashed sets: 13 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041950 none C=CCC(=O)N1CC=C(CNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [60, 26, 6, 1, 6, 1, 1, 1, 1, 1, 12, 55, 55, 55, 61, 61, 61, 61, 61, 1, 1, 60, 60, 60, 26, 26, 1, 1, 1, 12, 12, 55, 61, 1, 1, 1, 1] 201 rigid atoms, others: [33, 34, 3, 36, 5, 6, 7, 8, 9, 19, 20, 26, 27, 28, 35] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 29, 30, 31, 32]) total number of confs: 347 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041950 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041950 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041950/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041950 Building REAL250005041951 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041951' /scratch/stefan/7921153/working/building/REAL250005041951 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041951 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041951/0 /scratch/stefan/7921153/working/building/REAL250005041951 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 60) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/60 `/scratch/stefan/7921153/working/3D/60' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CCC(=O)N1CC=C(CNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005041951.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041951.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041951/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041951 none N#CCC(=O)N1CC=C(CNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 164, 72, 164, 72, 72, 72, 19, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 72, 72, 201, 201, 72, 72, 72, 18, 18, 4, 1, 72, 72, 72, 72] 201 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33]) total number of confs: 594 number of broken/clashed sets: 13 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041951 none N#CCC(=O)N1CC=C(CNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 1, 6, 1, 1, 1, 1, 1, 13, 61, 61, 61, 72, 72, 72, 72, 72, 1, 1, 26, 26, 1, 1, 1, 13, 13, 61, 72, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 3, 5, 6, 7, 8, 9, 19, 20, 23, 24, 25, 30, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 26, 27, 28, 29]) total number of confs: 272 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041951 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041951 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041951/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041951 Building REAL250005041952 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041952' /scratch/stefan/7921153/working/building/REAL250005041952 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041952 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041952/0 /scratch/stefan/7921153/working/building/REAL250005041952 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 61) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/61 `/scratch/stefan/7921153/working/3D/61' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCF)N1CC=C(CNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005041952.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041952.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041952/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041952 none O=C(CCF)N1CC=C(CNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'F', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 15, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 81, 160, 201, 201, 81, 81, 81, 20, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 81, 81, 201, 201, 201, 201, 81, 81, 81, 19, 19, 4, 1, 81, 81, 81, 81] 201 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 31] 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, 32, 33, 34, 35]) total number of confs: 615 number of broken/clashed sets: 16 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041952 none O=C(CCF)N1CC=C(CNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'F', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 15, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 19, 34, 1, 1, 1, 1, 1, 13, 61, 61, 61, 81, 81, 81, 81, 81, 1, 1, 19, 19, 33, 33, 1, 1, 1, 13, 13, 61, 81, 1, 1, 1, 1] 201 rigid atoms, others: [32, 1, 34, 33, 5, 6, 7, 8, 9, 19, 20, 25, 26, 27, 35] set([0, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 28, 29, 30, 31]) total number of confs: 345 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041952 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041952 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041952/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041952 Building REAL250005041953 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041953' /scratch/stefan/7921153/working/building/REAL250005041953 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041953 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041953/0 /scratch/stefan/7921153/working/building/REAL250005041953 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 62) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/62 `/scratch/stefan/7921153/working/3D/62' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](O)C(=O)N1CC=C(CNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005041953.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041953.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041953/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041953 none C[C@@H](O)C(=O)N1CC=C(CNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 459 conformations in input total number of sets (complete confs): 459 using faster count positions algorithm for large data unique positions, atoms: [153, 132, 153, 153, 87, 132, 87, 87, 87, 29, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 87, 87, 153, 153, 153, 459, 87, 87, 87, 28, 28, 7, 1, 87, 87, 87, 87] 459 rigid atoms, others: [32, 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, 33, 34, 35, 36]) total number of confs: 911 number of broken/clashed sets: 92 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041953 none C[C@@H](O)C(=O)N1CC=C(CNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 459 conformations in input total number of sets (complete confs): 459 using faster count positions algorithm for large data unique positions, atoms: [21, 7, 21, 21, 1, 7, 1, 1, 1, 1, 1, 13, 66, 66, 66, 87, 87, 87, 87, 87, 1, 1, 21, 21, 21, 63, 1, 1, 1, 13, 13, 66, 87, 1, 1, 1, 1] 459 rigid atoms, others: [33, 34, 35, 4, 6, 7, 8, 9, 10, 20, 21, 36, 26, 27, 28] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 29, 30, 31, 32]) total number of confs: 345 number of broken/clashed sets: 92 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041953 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041953 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041953/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041953 Building REAL250005041954 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041954' /scratch/stefan/7921153/working/building/REAL250005041954 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041954 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041954/0 /scratch/stefan/7921153/working/building/REAL250005041954 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 63) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/63 `/scratch/stefan/7921153/working/3D/63' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(=O)N1CC=C(CNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005041954.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041954.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041954/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041954 none C=CC(=O)N1CC=C(CNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 138 conformations in input total number of sets (complete confs): 138 using faster count positions algorithm for large data unique positions, atoms: [138, 138, 87, 138, 87, 87, 87, 26, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 87, 87, 138, 138, 138, 87, 87, 87, 26, 26, 7, 1, 87, 87, 87, 87] 138 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33]) total number of confs: 351 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041954 none C=CC(=O)N1CC=C(CNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 138 conformations in input total number of sets (complete confs): 138 using faster count positions algorithm for large data unique positions, atoms: [33, 7, 1, 7, 1, 1, 1, 1, 1, 13, 67, 67, 67, 87, 87, 87, 87, 87, 1, 1, 33, 33, 33, 1, 1, 1, 13, 13, 67, 87, 1, 1, 1, 1] 138 rigid atoms, others: [32, 33, 2, 4, 5, 6, 7, 8, 18, 19, 23, 24, 25, 30, 31] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 26, 27, 28, 29]) total number of confs: 286 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041954 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041954 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041954/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041954 Building REAL250005041955 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041955' /scratch/stefan/7921153/working/building/REAL250005041955 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041955 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041955/0 /scratch/stefan/7921153/working/building/REAL250005041955 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 64) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/64 `/scratch/stefan/7921153/working/3D/64' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)NC1CCC(C)N(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005041955.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041955.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041955/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041955 none CCC(=O)NC1CCC(C)N(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [32, 22, 22, 22, 13, 13, 13, 13, 13, 13, 9, 1, 9, 1, 1, 1, 1, 1, 1, 13, 32, 32, 32, 32, 32, 22, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 13, 13] 32 rigid atoms, others: [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, 34, 36, 37]) total number of confs: 119 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041955 none CCC(=O)NC1CCC(C)N(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [17, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 13, 13, 13, 13, 13, 1, 17, 17, 17, 17, 17, 6, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 1, 1] 32 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 37, 19, 36, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 33, 32, 12, 13, 14, 15, 16, 17, 18, 35, 20, 21, 22, 23, 24, 25, 34]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041955 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041955 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041955/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041955 Building REAL250005041956 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041956' /scratch/stefan/7921153/working/building/REAL250005041956 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041956 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041956/0 /scratch/stefan/7921153/working/building/REAL250005041956 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 65) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/65 `/scratch/stefan/7921153/working/3D/65' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC1CCC(C)N(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005041956.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041956.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041956/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041956 none CC(=O)NC1CCC(C)N(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 8, 8, 8, 8, 8, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 8, 12, 12, 12, 12, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 8, 8] 12 rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34]) total number of confs: 29 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041956 none CC(=O)NC1CCC(C)N(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 8, 8, 8, 8, 8, 1, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 1, 1] 12 rigid atoms, others: [33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 18, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 32, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 29, 30, 31]) total number of confs: 32 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041956 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041956 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041956/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041956 Building REAL250005041957 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041957' /scratch/stefan/7921153/working/building/REAL250005041957 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041957 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041957/0 /scratch/stefan/7921153/working/building/REAL250005041957 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 66) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/66 `/scratch/stefan/7921153/working/3D/66' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCC(NC(=O)C2CC2)CN1C(=O)C1=CC(=O)[N-]O1) `REAL250005041957.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041957.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041957/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041957 none CC1CCC(NC(=O)C2CC2)CN1C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', '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', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 12, 12, 14, 14, 14, 29, 29, 12, 9, 1, 9, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 14, 29, 29, 29, 29, 29, 12, 12, 1] 29 rigid atoms, others: [38, 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]) total number of confs: 78 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: REAL250005041957 none CC1CCC(NC(=O)C2CC2)CN1C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', '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', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 8, 8, 1, 8, 1, 1, 1, 15, 15, 15, 20, 20, 29, 29, 29, 29, 29, 15, 15, 15, 15, 15, 15, 15, 15, 15, 8, 1, 1, 1, 1, 1, 15, 15, 29] 29 rigid atoms, others: [32, 33, 34, 35, 6, 8, 9, 10, 31] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38]) total number of confs: 74 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041957 none CC1CCC(NC(=O)C2CC2)CN1C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', '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', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 5, 5, 15, 15, 1, 1, 1, 4, 4, 12, 12, 12, 12, 12, 2, 2, 2, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 15, 15, 1, 1, 12] 29 rigid atoms, others: [0, 1, 2, 3, 4, 5, 11, 12, 13, 37, 24, 25, 26, 27, 28, 29, 36] set([6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31, 32, 33, 34, 35, 38]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041957 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041957 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041957/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041957 Building REAL250005041958 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041958' /scratch/stefan/7921153/working/building/REAL250005041958 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041958 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041958/0 /scratch/stefan/7921153/working/building/REAL250005041958 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 67) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/67 `/scratch/stefan/7921153/working/3D/67' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)NC1CCC(C)N(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005041958.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041958.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041958/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041958 none COCC(=O)NC1CCC(C)N(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 27, 27, 27, 12, 12, 12, 12, 12, 12, 10, 1, 10, 1, 1, 1, 1, 1, 1, 12, 54, 54, 54, 54, 54, 27, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1, 12, 12] 54 rigid atoms, others: [36, 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, 37, 38]) total number of confs: 212 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041958 none COCC(=O)NC1CCC(C)N(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [30, 26, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 12, 12, 12, 12, 1, 30, 30, 30, 27, 27, 6, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 1, 1] 54 rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 11, 12, 38, 37, 20, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 33, 34, 35, 36]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041958 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041958 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041958/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041958 Building REAL250005041959 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041959' /scratch/stefan/7921153/working/building/REAL250005041959 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041959 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041959/0 /scratch/stefan/7921153/working/building/REAL250005041959 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 68) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/68 `/scratch/stefan/7921153/working/3D/68' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(=O)NC1CCC(C)N(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005041959.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041959.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041959/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041959 none CCCC(=O)NC1CCC(C)N(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 39, 39, 39, 17, 17, 17, 17, 17, 17, 11, 1, 11, 1, 1, 1, 1, 1, 1, 17, 72, 72, 72, 72, 72, 72, 72, 39, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 17, 17] 72 rigid atoms, others: [38, 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, 37, 39, 40]) total number of confs: 252 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041959 none CCCC(=O)NC1CCC(C)N(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [39, 33, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 17, 17, 17, 17, 17, 1, 41, 41, 41, 41, 41, 33, 33, 7, 1, 1, 1, 1, 1, 1, 2, 2, 2, 17, 1, 1] 72 rigid atoms, others: [32, 33, 34, 5, 6, 7, 8, 9, 10, 11, 12, 40, 20, 39, 29, 30, 31] set([0, 1, 2, 3, 4, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 35, 36, 37, 38]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041959 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041959 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041959/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041959 Building REAL250005041960 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041960' /scratch/stefan/7921153/working/building/REAL250005041960 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041960 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041960/0 /scratch/stefan/7921153/working/building/REAL250005041960 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 69) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/69 `/scratch/stefan/7921153/working/3D/69' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)NC1CCC(C)N(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005041960.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041960.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041960/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041960 none CC(C)C(=O)NC1CCC(C)N(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [34, 31, 34, 31, 31, 18, 18, 18, 18, 18, 18, 11, 1, 11, 1, 1, 1, 1, 1, 1, 18, 34, 34, 34, 34, 34, 34, 34, 31, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 18, 18] 34 rigid atoms, others: [38, 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, 37, 39, 40]) total number of confs: 90 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041960 none CC(C)C(=O)NC1CCC(C)N(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [19, 7, 19, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 18, 18, 18, 18, 18, 1, 19, 19, 19, 19, 19, 19, 19, 7, 1, 1, 1, 1, 1, 1, 2, 2, 2, 18, 1, 1] 34 rigid atoms, others: [32, 33, 34, 5, 6, 7, 8, 9, 10, 11, 12, 40, 20, 39, 29, 30, 31] set([0, 1, 2, 3, 4, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 35, 36, 37, 38]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041960 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041960 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041960/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041960 Building REAL250005041961 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041961' /scratch/stefan/7921153/working/building/REAL250005041961 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041961 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041961/0 /scratch/stefan/7921153/working/building/REAL250005041961 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 70) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/70 `/scratch/stefan/7921153/working/3D/70' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCC(NC(=O)C(N)=O)CN1C(=O)C1=CC(=O)[N-]O1) `REAL250005041961.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041961/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041961 none CC1CCC(NC(=O)C(N)=O)CN1C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.am', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 1, 8, 11, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 6, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 7, 7, 7, 8, 8, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 8, 8, 5, 5, 1] 8 rigid atoms, others: [35, 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]) total number of confs: 21 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041961 none CC1CCC(NC(=O)C(N)=O)CN1C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.am', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 1, 8, 11, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 6, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 1, 1, 1, 3, 3, 5, 5, 5, 5, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 5, 7, 7, 1, 1, 5] 8 rigid atoms, others: [0, 1, 2, 3, 4, 5, 33, 11, 12, 34, 13, 24, 25, 26, 27, 28, 29] set([32, 35, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31]) total number of confs: 35 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041961 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041961 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041961/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041961 Building REAL250005041962 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041962' /scratch/stefan/7921153/working/building/REAL250005041962 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041962 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041962/0 /scratch/stefan/7921153/working/building/REAL250005041962 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 71) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/71 `/scratch/stefan/7921153/working/3D/71' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC(=O)NC1CCC(C)N(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005041962.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041962.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041962/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041962 none C=CCC(=O)NC1CCC(C)N(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 24, 24, 24, 13, 13, 13, 13, 13, 13, 10, 1, 10, 1, 1, 1, 1, 1, 1, 13, 54, 54, 54, 54, 54, 24, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 13, 13] 54 rigid atoms, others: [36, 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, 37, 38]) total number of confs: 188 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041962 none C=CCC(=O)NC1CCC(C)N(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [37, 28, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 13, 13, 13, 13, 13, 1, 37, 37, 37, 28, 28, 6, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 1, 1] 54 rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 11, 12, 38, 37, 20, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 33, 34, 35, 36]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041962 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041962 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041962/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041962 Building REAL250005041963 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041963' /scratch/stefan/7921153/working/building/REAL250005041963 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041963 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041963/0 /scratch/stefan/7921153/working/building/REAL250005041963 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 72) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/72 `/scratch/stefan/7921153/working/3D/72' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCC(NC(=O)CO)CN1C(=O)C1=CC(=O)[N-]O1) `REAL250005041963.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041963.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041963/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041963 none CC1CCC(NC(=O)CO)CN1C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 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, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [10, 10, 10, 10, 10, 10, 16, 16, 16, 19, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 16, 19, 19, 57, 10, 10, 1] 57 rigid atoms, others: [35, 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]) total number of confs: 114 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041963 none CC1CCC(NC(=O)CO)CN1C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 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, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 6, 12, 1, 1, 1, 3, 3, 10, 10, 10, 10, 10, 2, 2, 2, 1, 1, 1, 1, 1, 1, 6, 12, 12, 36, 1, 1, 10] 57 rigid atoms, others: [0, 1, 2, 3, 4, 5, 33, 10, 11, 12, 34, 23, 24, 25, 26, 27, 28] set([32, 35, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041963 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041963 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041963/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041963 Building REAL250005041964 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041964' /scratch/stefan/7921153/working/building/REAL250005041964 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041964 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041964/0 /scratch/stefan/7921153/working/building/REAL250005041964 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 73) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/73 `/scratch/stefan/7921153/working/3D/73' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)C(=O)NC1CCC(C)N(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005041964.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041964.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041964/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041964 none CC(O)C(=O)NC1CCC(C)N(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [19, 13, 19, 13, 13, 10, 10, 10, 10, 10, 10, 8, 1, 8, 1, 1, 1, 1, 1, 1, 10, 19, 19, 19, 19, 57, 13, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 10, 10] 57 rigid atoms, others: [36, 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, 37, 38]) total number of confs: 118 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041964 none CC(O)C(=O)NC1CCC(C)N(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [13, 4, 13, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 10, 10, 10, 10, 10, 1, 13, 13, 13, 13, 39, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 1, 1] 57 rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 11, 12, 38, 37, 20, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 33, 34, 35, 36]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041964 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041964 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041964/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041964 Building REAL250005041965 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041965' /scratch/stefan/7921153/working/building/REAL250005041965 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041965 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041965/0 /scratch/stefan/7921153/working/building/REAL250005041965 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 74) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/74 `/scratch/stefan/7921153/working/3D/74' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCC(NC(=O)CCF)CN1C(=O)C1=CC(=O)[N-]O1) `REAL250005041965.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041965/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041965 none CC1CCC(NC(=O)CCF)CN1C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 15, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [15, 15, 15, 15, 15, 15, 33, 33, 33, 72, 72, 15, 10, 1, 10, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 33, 72, 72, 72, 72, 15, 15, 1] 72 rigid atoms, others: [37, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 260 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041965 none CC1CCC(NC(=O)CCF)CN1C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 15, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 7, 7, 37, 45, 1, 1, 1, 3, 3, 15, 15, 15, 15, 15, 2, 2, 2, 1, 1, 1, 1, 1, 1, 7, 37, 37, 45, 45, 1, 1, 15] 72 rigid atoms, others: [0, 1, 2, 3, 4, 5, 11, 12, 13, 35, 24, 25, 26, 27, 28, 29, 36] set([32, 33, 34, 37, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041965 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041965 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041965/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041965 Building REAL250005041966 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041966' /scratch/stefan/7921153/working/building/REAL250005041966 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041966 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041966/0 /scratch/stefan/7921153/working/building/REAL250005041966 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 75) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/75 `/scratch/stefan/7921153/working/3D/75' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](O)C(=O)NC1CCC(C)N(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005041966.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041966.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041966/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041966 none C[C@@H](O)C(=O)NC1CCC(C)N(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [34, 22, 34, 34, 22, 22, 14, 14, 14, 14, 14, 14, 11, 1, 11, 1, 1, 1, 1, 1, 1, 14, 34, 34, 34, 102, 22, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 14, 14] 102 rigid atoms, others: [36, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 215 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041966 none C[C@@H](O)C(=O)NC1CCC(C)N(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [23, 6, 23, 22, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 14, 14, 14, 14, 14, 1, 23, 23, 23, 69, 6, 1, 1, 1, 1, 1, 1, 2, 2, 2, 14, 1, 1] 102 rigid atoms, others: [32, 37, 6, 7, 8, 9, 10, 11, 12, 13, 38, 21, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 33, 34, 35, 36]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041966 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041966 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041966/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041966 Building REAL250005041967 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041967' /scratch/stefan/7921153/working/building/REAL250005041967 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041967 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041967/0 /scratch/stefan/7921153/working/building/REAL250005041967 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 76) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/76 `/scratch/stefan/7921153/working/3D/76' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](O)C(=O)NC1CCC(C)N(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005041967.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041967.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041967/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041967 none C[C@H](O)C(=O)NC1CCC(C)N(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [19, 13, 19, 19, 13, 13, 10, 10, 10, 10, 10, 10, 8, 1, 8, 1, 1, 1, 1, 1, 1, 10, 19, 19, 19, 57, 13, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 10, 10] 57 rigid atoms, others: [36, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 118 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041967 none C[C@H](O)C(=O)NC1CCC(C)N(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [13, 4, 13, 13, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 10, 10, 10, 10, 10, 1, 13, 13, 13, 39, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 1, 1] 57 rigid atoms, others: [32, 37, 6, 7, 8, 9, 10, 11, 12, 13, 38, 21, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 33, 34, 35, 36]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041967 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041967 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041967/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041967 Building REAL250005041968 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041968' /scratch/stefan/7921153/working/building/REAL250005041968 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041968 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041968/0 /scratch/stefan/7921153/working/building/REAL250005041968 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 77) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/77 `/scratch/stefan/7921153/working/3D/77' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=CC(=O)NC1CCC(C)N(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005041968.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041968.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041968/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041968 none CC=CC(=O)NC1CCC(C)N(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 13, 13, 13, 10, 10, 10, 10, 10, 10, 8, 1, 8, 1, 1, 1, 1, 1, 1, 10, 18, 18, 18, 18, 18, 13, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 10, 10] 18 rigid atoms, others: [36, 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, 37, 38]) total number of confs: 51 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041968 none CC=CC(=O)NC1CCC(C)N(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 10, 10, 10, 10, 1, 13, 13, 13, 13, 13, 5, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 1, 1] 18 rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 11, 12, 38, 37, 20, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 33, 34, 35, 36]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041968 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041968 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041968/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041968 Building REAL250005041969 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041969' /scratch/stefan/7921153/working/building/REAL250005041969 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041969 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041969/0 /scratch/stefan/7921153/working/building/REAL250005041969 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 78) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/78 `/scratch/stefan/7921153/working/3D/78' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)N1CC(NC(=O)C2=CC(=O)[N-]O2)CCC1C) `REAL250005041969.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041969.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041969/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041969 none COCC(=O)N1CC(NC(=O)C2=CC(=O)[N-]O2)CCC1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 26, 16, 26, 16, 16, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 52, 52, 52, 52, 52, 16, 16, 16, 7, 1, 16, 16, 16, 16, 16, 16, 16, 16] 52 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 196 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041969 none COCC(=O)N1CC(NC(=O)C2=CC(=O)[N-]O2)CCC1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [29, 16, 4, 1, 4, 1, 1, 1, 1, 7, 7, 7, 16, 16, 16, 16, 16, 1, 1, 1, 1, 29, 29, 29, 16, 16, 1, 1, 1, 7, 16, 1, 1, 1, 1, 1, 2, 2, 2] 52 rigid atoms, others: [32, 33, 34, 3, 5, 6, 7, 8, 35, 17, 18, 19, 20, 26, 27, 28, 31] set([0, 1, 2, 4, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 29, 30, 36, 37, 38]) total number of confs: 106 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041969 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041969 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041969/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041969 Building REAL250005041970 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041970' /scratch/stefan/7921153/working/building/REAL250005041970 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041970 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041970/0 /scratch/stefan/7921153/working/building/REAL250005041970 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 79) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/79 `/scratch/stefan/7921153/working/3D/79' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(=O)N1CC(NC(=O)C2=CC(=O)[N-]O2)CCC1C) `REAL250005041970.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041970.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041970/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041970 none CCCC(=O)N1CC(NC(=O)C2=CC(=O)[N-]O2)CCC1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [48, 45, 22, 13, 22, 13, 13, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 48, 48, 48, 48, 48, 45, 45, 13, 13, 13, 5, 1, 13, 13, 13, 13, 13, 13, 13, 13] 48 rigid atoms, others: [32, 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, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 192 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041970 none CCCC(=O)N1CC(NC(=O)C2=CC(=O)[N-]O2)CCC1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [20, 14, 3, 1, 3, 1, 1, 1, 1, 7, 7, 7, 13, 13, 13, 13, 13, 1, 1, 1, 1, 21, 21, 21, 21, 21, 14, 14, 1, 1, 1, 7, 13, 1, 1, 1, 1, 1, 2, 2, 2] 48 rigid atoms, others: [33, 34, 3, 36, 5, 6, 7, 8, 17, 18, 19, 20, 37, 28, 29, 30, 35] set([0, 1, 2, 4, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 31, 32, 38, 39, 40]) total number of confs: 126 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041970 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041970 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041970/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041970 Building REAL250005041971 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041971' /scratch/stefan/7921153/working/building/REAL250005041971 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041971 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041971/0 /scratch/stefan/7921153/working/building/REAL250005041971 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 80) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/80 `/scratch/stefan/7921153/working/3D/80' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N1CC(NC(=O)C2=CC(=O)[N-]O2)CCC1C) `REAL250005041971.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041971.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041971/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041971 none CC(C)C(=O)N1CC(NC(=O)C2=CC(=O)[N-]O2)CCC1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 15, 19, 10, 15, 10, 10, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 19, 19, 19, 19, 19, 19, 19, 10, 10, 10, 7, 1, 10, 10, 10, 10, 10, 10, 10, 10] 19 rigid atoms, others: [32, 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, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 67 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041971 none CC(C)C(=O)N1CC(NC(=O)C2=CC(=O)[N-]O2)CCC1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [7, 3, 7, 1, 3, 1, 1, 1, 1, 6, 6, 6, 10, 10, 10, 10, 10, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 6, 10, 1, 1, 1, 1, 1, 2, 2, 2] 19 rigid atoms, others: [33, 34, 3, 36, 5, 6, 7, 8, 17, 18, 19, 20, 37, 28, 29, 30, 35] set([0, 1, 2, 4, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 31, 32, 38, 39, 40]) total number of confs: 49 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041971 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041971 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041971/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041971 Building REAL250005041972 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041972' /scratch/stefan/7921153/working/building/REAL250005041972 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041972 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041972/0 /scratch/stefan/7921153/working/building/REAL250005041972 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 81) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/81 `/scratch/stefan/7921153/working/3D/81' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N1CC(NC(=O)C2=CC(=O)[N-]O2)CCC1C) `REAL250005041972.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041972/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041972 none CCC(=O)N1CC(NC(=O)C2=CC(=O)[N-]O2)CCC1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 19, 15, 19, 15, 15, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 23, 23, 23, 23, 23, 15, 15, 15, 7, 1, 15, 15, 15, 15, 15, 15, 15, 15] 23 rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 77 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041972 none CCC(=O)N1CC(NC(=O)C2=CC(=O)[N-]O2)CCC1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 3, 1, 3, 1, 1, 1, 1, 7, 7, 7, 15, 15, 15, 15, 15, 1, 1, 1, 1, 9, 9, 9, 9, 9, 1, 1, 1, 7, 15, 1, 1, 1, 1, 1, 2, 2, 2] 23 rigid atoms, others: [32, 33, 2, 4, 5, 6, 7, 34, 16, 17, 18, 19, 25, 26, 27, 30, 31] set([0, 1, 3, 36, 37, 8, 9, 10, 11, 12, 13, 14, 15, 35, 20, 21, 22, 23, 24, 28, 29]) total number of confs: 64 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041972 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041972 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041972/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041972 Building REAL250005041973 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041973' /scratch/stefan/7921153/working/building/REAL250005041973 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041973 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041973/0 /scratch/stefan/7921153/working/building/REAL250005041973 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 82) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/82 `/scratch/stefan/7921153/working/3D/82' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CC(NC(=O)C2=CC(=O)[N-]O2)CCC1C) `REAL250005041973.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041973.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041973/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041973 none CC(=O)N1CC(NC(=O)C2=CC(=O)[N-]O2)CCC1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 7, 1, 10, 10, 10, 10, 10, 10, 10, 10] 10 rigid atoms, others: [7, 9, 10, 11, 12, 13, 14, 26] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 25 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041973 none CC(=O)N1CC(NC(=O)C2=CC(=O)[N-]O2)CCC1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 5, 5, 5, 10, 10, 10, 10, 10, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 5, 10, 1, 1, 1, 1, 1, 2, 2, 2] 10 rigid atoms, others: [1, 3, 4, 5, 6, 15, 16, 17, 18, 22, 23, 24, 27, 28, 29, 30, 31] set([0, 32, 2, 34, 33, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 25, 26]) total number of confs: 30 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041973 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041973 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041973/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041973 Building REAL250005041974 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041974' /scratch/stefan/7921153/working/building/REAL250005041974 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041974 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041974/0 /scratch/stefan/7921153/working/building/REAL250005041974 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 83) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/83 `/scratch/stefan/7921153/working/3D/83' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCC(NC(=O)C2=CC(=O)[N-]O2)CN1C(=O)C1CC1) `REAL250005041974.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041974/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041974 none CC1CCC(NC(=O)C2=CC(=O)[N-]O2)CN1C(=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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] 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: [9, 9, 9, 9, 9, 9, 19, 19, 19, 22, 22, 22, 22, 22, 9, 8, 1, 8, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 19, 22, 9, 9, 1, 1, 1, 1, 1] 22 rigid atoms, others: [34, 35, 36, 37, 38, 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]) total number of confs: 53 number of broken/clashed sets: 1 ./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: REAL250005041974 none CC1CCC(NC(=O)C2=CC(=O)[N-]O2)CN1C(=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 13, 13, 13, 18, 18, 22, 22, 13, 13, 13, 13, 13, 13, 13, 13, 13, 7, 1, 13, 13, 22, 22, 22, 22, 22] 22 rigid atoms, others: [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, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 67 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041974 none CC1CCC(NC(=O)C2=CC(=O)[N-]O2)CN1C(=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 7, 7, 13, 13, 13, 13, 13, 1, 1, 1, 3, 3, 9, 9, 2, 2, 2, 1, 1, 1, 1, 1, 1, 7, 13, 1, 1, 9, 9, 9, 9, 9] 22 rigid atoms, others: [0, 1, 2, 3, 4, 5, 16, 32, 14, 15, 33, 24, 25, 26, 27, 28, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 30, 31, 34, 35, 36, 37, 38]) total number of confs: 53 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041974 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041974 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041974/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041974 Building REAL250005041975 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041975' /scratch/stefan/7921153/working/building/REAL250005041975 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041975 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041975/0 /scratch/stefan/7921153/working/building/REAL250005041975 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 84) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/84 `/scratch/stefan/7921153/working/3D/84' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCC(NC(=O)C2=CC(=O)[N-]O2)CN1C(=O)C(N)=O) `REAL250005041975.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041975/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041975 none CC1CCC(NC(=O)C2=CC(=O)[N-]O2)CN1C(=O)C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 11, 11, 18, 18, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 1, 7, 7, 18, 18] 18 rigid atoms, others: [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, 32, 33, 34, 35]) total number of confs: 61 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041975 none CC1CCC(NC(=O)C2=CC(=O)[N-]O2)CN1C(=O)C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 6, 7, 7, 7, 7, 7, 1, 1, 1, 3, 3, 8, 8, 2, 2, 2, 1, 1, 1, 1, 1, 1, 6, 7, 1, 1, 8, 8] 18 rigid atoms, others: [0, 1, 2, 3, 4, 5, 16, 32, 14, 15, 33, 24, 25, 26, 27, 28, 29] set([34, 35, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 30, 31]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041975 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041975 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041975/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041975 Building REAL250005041976 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041976' /scratch/stefan/7921153/working/building/REAL250005041976 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041976 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041976/0 /scratch/stefan/7921153/working/building/REAL250005041976 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 85) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/85 `/scratch/stefan/7921153/working/3D/85' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCC(NC(=O)C2=CC(=O)[N-]O2)CN1C(=O)CO) `REAL250005041976.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041976/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041976 none CC1CCC(NC(=O)C2=CC(=O)[N-]O2)CN1C(=O)CO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 12, 7, 7, 7, 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, 3, 7, 3, 7, 7, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 13, 13, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 13, 13, 13, 18, 18, 22, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 1, 13, 13, 22, 22, 66] 66 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 30] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35]) total number of confs: 141 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041976 none CC1CCC(NC(=O)C2=CC(=O)[N-]O2)CN1C(=O)CO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 12, 7, 7, 7, 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, 3, 7, 3, 7, 7, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 7, 7, 13, 13, 13, 13, 13, 1, 1, 1, 3, 3, 9, 2, 2, 2, 1, 1, 1, 1, 1, 1, 7, 13, 1, 1, 9, 9, 27] 66 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 14, 15, 16, 23, 24, 25, 26, 27, 28, 31] set([33, 34, 35, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 29, 30]) total number of confs: 89 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041976 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041976 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041976/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041976 Building REAL250005041977 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041977' /scratch/stefan/7921153/working/building/REAL250005041977 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041977 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041977/0 /scratch/stefan/7921153/working/building/REAL250005041977 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 86) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/86 `/scratch/stefan/7921153/working/3D/86' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)C(=O)N1CC(NC(=O)C2=CC(=O)[N-]O2)CCC1C) `REAL250005041977.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041977/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041977 none CC(O)C(=O)N1CC(NC(=O)C2=CC(=O)[N-]O2)CCC1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [20, 11, 20, 7, 11, 7, 7, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 20, 20, 20, 20, 60, 7, 7, 7, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7] 60 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 138 number of broken/clashed sets: 23 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041977 none CC(O)C(=O)N1CC(NC(=O)C2=CC(=O)[N-]O2)CCC1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [10, 3, 10, 1, 3, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 1, 1, 1, 1, 10, 10, 10, 10, 30, 1, 1, 1, 5, 7, 1, 1, 1, 1, 1, 2, 2, 2] 60 rigid atoms, others: [32, 33, 34, 3, 5, 6, 7, 8, 35, 17, 18, 19, 20, 26, 27, 28, 31] set([0, 1, 2, 4, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 29, 30, 36, 37, 38]) total number of confs: 83 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041977 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041977 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041977/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041977 Building REAL250005041978 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041978' /scratch/stefan/7921153/working/building/REAL250005041978 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041978 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041978/0 /scratch/stefan/7921153/working/building/REAL250005041978 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 87) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/87 `/scratch/stefan/7921153/working/3D/87' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)C(=O)N1CC(NC(=O)C2=CC(=O)[N-]O2)CCC1C) `REAL250005041978.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041978.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041978/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041978 none CC(=O)C(=O)N1CC(NC(=O)C2=CC(=O)[N-]O2)CCC1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 12, 20, 7, 12, 7, 7, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 20, 20, 20, 7, 7, 7, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7] 20 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 69 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041978 none CC(=O)C(=O)N1CC(NC(=O)C2=CC(=O)[N-]O2)CCC1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 3, 9, 1, 3, 1, 1, 1, 1, 6, 6, 6, 7, 7, 7, 7, 7, 1, 1, 1, 1, 9, 9, 9, 1, 1, 1, 6, 7, 1, 1, 1, 1, 1, 2, 2, 2] 20 rigid atoms, others: [32, 33, 3, 5, 6, 7, 8, 17, 18, 19, 20, 24, 25, 26, 29, 30, 31] set([0, 1, 2, 34, 4, 9, 10, 11, 12, 13, 14, 15, 16, 35, 21, 22, 23, 36, 27, 28]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041978 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041978 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041978/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041978 Building REAL250005041979 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041979' /scratch/stefan/7921153/working/building/REAL250005041979 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041979 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041979/0 /scratch/stefan/7921153/working/building/REAL250005041979 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 88) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/88 `/scratch/stefan/7921153/working/3D/88' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=CC(=O)N1CC(NC(=O)C2=CC(=O)[N-]O2)CCC1C) `REAL250005041979.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041979/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041979 none CC=CC(=O)N1CC(NC(=O)C2=CC(=O)[N-]O2)CCC1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 16, 11, 16, 11, 11, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 20, 20, 20, 20, 20, 11, 11, 11, 6, 1, 11, 11, 11, 11, 11, 11, 11, 11] 20 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 65 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041979 none CC=CC(=O)N1CC(NC(=O)C2=CC(=O)[N-]O2)CCC1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [10, 10, 3, 1, 3, 1, 1, 1, 1, 6, 6, 6, 11, 11, 11, 11, 11, 1, 1, 1, 1, 10, 10, 10, 10, 10, 1, 1, 1, 6, 11, 1, 1, 1, 1, 1, 2, 2, 2] 20 rigid atoms, others: [32, 33, 34, 3, 5, 6, 7, 8, 35, 17, 18, 19, 20, 26, 27, 28, 31] set([0, 1, 2, 4, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 29, 30, 36, 37, 38]) total number of confs: 52 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041979 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041979 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041979/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041979 Building REAL250005041980 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041980' /scratch/stefan/7921153/working/building/REAL250005041980 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041980 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041980/0 /scratch/stefan/7921153/working/building/REAL250005041980 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 89) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/89 `/scratch/stefan/7921153/working/3D/89' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](O)C(=O)N1CC(NC(=O)C2=CC(=O)[N-]O2)CCC1C) `REAL250005041980.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041980/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041980 none C[C@H](O)C(=O)N1CC(NC(=O)C2=CC(=O)[N-]O2)CCC1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [12, 10, 12, 12, 7, 10, 7, 7, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 12, 12, 12, 36, 7, 7, 7, 6, 1, 7, 7, 7, 7, 7, 7, 7, 7] 36 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 77 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041980 none C[C@H](O)C(=O)N1CC(NC(=O)C2=CC(=O)[N-]O2)CCC1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 6, 6, 1, 3, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 1, 1, 1, 1, 6, 6, 6, 18, 1, 1, 1, 5, 7, 1, 1, 1, 1, 1, 2, 2, 2] 36 rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 18, 19, 20, 21, 26, 27, 28, 31] set([0, 1, 2, 3, 5, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 29, 30, 36, 37, 38]) total number of confs: 60 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041980 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041980 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041980/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041980 Building REAL250005041981 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041981' /scratch/stefan/7921153/working/building/REAL250005041981 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041981 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041981/0 /scratch/stefan/7921153/working/building/REAL250005041981 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 90) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/90 `/scratch/stefan/7921153/working/3D/90' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC(=O)N1CC(NC(=O)C2=CC(=O)[N-]O2)CCC1C) `REAL250005041981.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041981/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041981 none C=CCC(=O)N1CC(NC(=O)C2=CC(=O)[N-]O2)CCC1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 27, 17, 27, 17, 17, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 45, 45, 45, 45, 45, 17, 17, 17, 6, 1, 17, 17, 17, 17, 17, 17, 17, 17] 45 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 171 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041981 none C=CCC(=O)N1CC(NC(=O)C2=CC(=O)[N-]O2)CCC1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [26, 12, 3, 1, 3, 1, 1, 1, 1, 7, 7, 7, 17, 17, 17, 17, 17, 1, 1, 1, 1, 26, 26, 26, 12, 12, 1, 1, 1, 7, 17, 1, 1, 1, 1, 1, 2, 2, 2] 45 rigid atoms, others: [32, 33, 34, 3, 5, 6, 7, 8, 35, 17, 18, 19, 20, 26, 27, 28, 31] set([0, 1, 2, 4, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 29, 30, 36, 37, 38]) total number of confs: 118 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041981 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041981 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041981/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041981 Building REAL250005041982 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041982' /scratch/stefan/7921153/working/building/REAL250005041982 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041982 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041982/0 /scratch/stefan/7921153/working/building/REAL250005041982 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 91) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/91 `/scratch/stefan/7921153/working/3D/91' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCC(NC(=O)C2=CC(=O)[N-]O2)CN1C(=O)CC#N) `REAL250005041982.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041982.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041982/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041982 none CC1CCC(NC(=O)C2=CC(=O)[N-]O2)CN1C(=O)CC#N NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.1', 'N.1', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 11, 11, 11, 15, 15, 29, 29, 11, 11, 11, 11, 11, 11, 11, 11, 11, 7, 1, 11, 11, 29, 29] 29 rigid atoms, others: [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, 32, 33, 34, 35]) total number of confs: 112 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041982 none CC1CCC(NC(=O)C2=CC(=O)[N-]O2)CN1C(=O)CC#N NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.1', 'N.1', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 6, 11, 11, 11, 11, 11, 1, 1, 1, 3, 3, 14, 14, 2, 2, 2, 1, 1, 1, 1, 1, 1, 6, 11, 1, 1, 14, 14] 29 rigid atoms, others: [0, 1, 2, 3, 4, 5, 16, 32, 14, 15, 33, 24, 25, 26, 27, 28, 29] set([34, 35, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 30, 31]) total number of confs: 71 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041982 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041982 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041982/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041982 Building REAL250005041983 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041983' /scratch/stefan/7921153/working/building/REAL250005041983 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041983 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041983/0 /scratch/stefan/7921153/working/building/REAL250005041983 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 92) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/92 `/scratch/stefan/7921153/working/3D/92' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCC(NC(=O)C2=CC(=O)[N-]O2)CN1C(=O)CCF) `REAL250005041983.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041983.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041983/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041983 none CC1CCC(NC(=O)C2=CC(=O)[N-]O2)CN1C(=O)CCF NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 18, 18, 18, 26, 26, 45, 45, 18, 18, 18, 18, 18, 18, 18, 18, 18, 8, 1, 18, 18, 45, 45, 45, 45] 45 rigid atoms, others: [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, 32, 33, 34, 35, 36, 37]) total number of confs: 159 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041983 none CC1CCC(NC(=O)C2=CC(=O)[N-]O2)CN1C(=O)CCF NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 7, 7, 18, 18, 18, 18, 18, 1, 1, 1, 3, 3, 12, 20, 2, 2, 2, 1, 1, 1, 1, 1, 1, 7, 18, 1, 1, 12, 12, 20, 20] 45 rigid atoms, others: [0, 1, 2, 3, 4, 5, 16, 32, 14, 15, 33, 24, 25, 26, 27, 28, 29] set([34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 30, 31]) total number of confs: 118 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041983 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041983 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041983/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041983 Building REAL250005041984 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041984' /scratch/stefan/7921153/working/building/REAL250005041984 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041984 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041984/0 /scratch/stefan/7921153/working/building/REAL250005041984 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 93) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/93 `/scratch/stefan/7921153/working/3D/93' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](O)C(=O)N1CC(NC(=O)C2=CC(=O)[N-]O2)CCC1C) `REAL250005041984.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041984.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041984/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041984 none C[C@@H](O)C(=O)N1CC(NC(=O)C2=CC(=O)[N-]O2)CCC1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [21, 15, 21, 21, 10, 15, 10, 10, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 21, 21, 21, 63, 10, 10, 10, 6, 1, 10, 10, 10, 10, 10, 10, 10, 10] 63 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 136 number of broken/clashed sets: 16 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041984 none C[C@@H](O)C(=O)N1CC(NC(=O)C2=CC(=O)[N-]O2)CCC1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [10, 3, 10, 10, 1, 3, 1, 1, 1, 1, 7, 7, 7, 10, 10, 10, 10, 10, 1, 1, 1, 1, 10, 10, 10, 30, 1, 1, 1, 7, 10, 1, 1, 1, 1, 1, 2, 2, 2] 63 rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 18, 19, 20, 21, 26, 27, 28, 31] set([0, 1, 2, 3, 5, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 29, 30, 36, 37, 38]) total number of confs: 89 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041984 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041984 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041984/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041984 Building REAL250005041985 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041985' /scratch/stefan/7921153/working/building/REAL250005041985 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041985 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041985/0 /scratch/stefan/7921153/working/building/REAL250005041985 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 94) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/94 `/scratch/stefan/7921153/working/3D/94' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(=O)N1CC(NC(=O)C2=CC(=O)[N-]O2)CCC1C) `REAL250005041985.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041985.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041985/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041985 none C=CC(=O)N1CC(NC(=O)C2=CC(=O)[N-]O2)CCC1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 13, 17, 13, 13, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 17, 17, 17, 13, 13, 13, 7, 1, 13, 13, 13, 13, 13, 13, 13, 13] 17 rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 49 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041985 none C=CC(=O)N1CC(NC(=O)C2=CC(=O)[N-]O2)CCC1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [7, 3, 1, 3, 1, 1, 1, 1, 7, 7, 7, 13, 13, 13, 13, 13, 1, 1, 1, 1, 7, 7, 7, 1, 1, 1, 7, 13, 1, 1, 1, 1, 1, 2, 2, 2] 17 rigid atoms, others: [32, 2, 4, 5, 6, 7, 16, 17, 18, 19, 23, 24, 25, 28, 29, 30, 31] set([0, 1, 34, 3, 33, 8, 9, 10, 11, 12, 13, 14, 15, 35, 20, 21, 22, 26, 27]) total number of confs: 49 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041985 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041985 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041985/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041985 Building REAL250005041986 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041986' /scratch/stefan/7921153/working/building/REAL250005041986 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041986 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041986/0 /scratch/stefan/7921153/working/building/REAL250005041986 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 95) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/95 `/scratch/stefan/7921153/working/3D/95' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N1CCC(C)C(CNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005041986.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041986.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041986/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041986 none CCC(=O)N1CCC(C)C(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 40, 72, 40, 40, 40, 40, 40, 19, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 40, 72, 72, 72, 72, 72, 40, 40, 40, 40, 40, 40, 40, 40, 40, 19, 19, 5, 1, 40, 40] 72 rigid atoms, others: [38, 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, 37, 39, 40]) total number of confs: 227 number of broken/clashed sets: 18 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041986 none CCC(=O)N1CCC(C)C(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [17, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 8, 33, 33, 33, 40, 40, 40, 40, 40, 1, 18, 18, 18, 17, 17, 1, 1, 1, 1, 1, 2, 2, 2, 1, 8, 8, 33, 40, 1, 1] 72 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 39, 34, 40, 20, 26, 27, 28, 29, 30] set([0, 1, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 31, 32, 33, 35, 36, 37, 38]) total number of confs: 173 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041986 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041986 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041986/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041986 Building REAL250005041987 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041987' /scratch/stefan/7921153/working/building/REAL250005041987 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041987 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041987/0 /scratch/stefan/7921153/working/building/REAL250005041987 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 96) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/96 `/scratch/stefan/7921153/working/3D/96' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCC(C)C(CNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005041987.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041987.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041987/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041987 none CC(=O)N1CCC(C)C(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [43, 33, 43, 33, 33, 33, 33, 33, 19, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 33, 43, 43, 43, 33, 33, 33, 33, 33, 33, 33, 33, 33, 19, 19, 8, 1, 33, 33] 43 rigid atoms, others: [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, 34, 36, 37]) total number of confs: 145 number of broken/clashed sets: 24 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041987 none CC(=O)N1CCC(C)C(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 7, 26, 26, 26, 33, 33, 33, 33, 33, 1, 5, 5, 5, 1, 1, 1, 1, 1, 2, 2, 2, 1, 7, 7, 26, 33, 1, 1] 43 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 19, 23, 24, 25, 26, 27, 36, 37, 31] set([0, 32, 2, 34, 33, 10, 11, 12, 13, 14, 15, 16, 17, 18, 35, 20, 21, 22, 28, 29, 30]) total number of confs: 101 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041987 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041987 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041987/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041987 Building REAL250005041988 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041988' /scratch/stefan/7921153/working/building/REAL250005041988 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041988 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041988/0 /scratch/stefan/7921153/working/building/REAL250005041988 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 97) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/97 `/scratch/stefan/7921153/working/3D/97' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCN(C(=O)CO)CC1CNC(=O)C1=CC(=O)[N-]O1) `REAL250005041988.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041988.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041988/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041988 none CC1CCN(C(=O)CO)CC1CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 156 conformations in input total number of sets (complete confs): 156 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 35, 35, 35, 35, 51, 51, 52, 35, 20, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 35, 35, 35, 35, 52, 52, 156, 35, 35, 35, 20, 20, 7, 1] 156 rigid atoms, others: [38, 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]) total number of confs: 336 number of broken/clashed sets: 49 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041988 none CC1CCN(C(=O)CO)CC1CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 156 conformations in input total number of sets (complete confs): 156 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 5, 13, 1, 1, 1, 6, 25, 25, 25, 35, 35, 35, 35, 35, 2, 2, 2, 1, 1, 1, 1, 1, 13, 13, 39, 1, 1, 1, 6, 6, 25, 35] 156 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 9, 10, 11, 34, 33, 24, 25, 26, 27, 28] set([6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 35, 36, 37, 38]) total number of confs: 176 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041988 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041988 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041988/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041988 Building REAL250005041989 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041989' /scratch/stefan/7921153/working/building/REAL250005041989 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041989 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041989/0 /scratch/stefan/7921153/working/building/REAL250005041989 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 98) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/98 `/scratch/stefan/7921153/working/3D/98' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)NCC1CN(C(=O)C2=CC(=O)[N-]O2)CCC1C) `REAL250005041989.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041989/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041989 none CCC(=O)NCC1CN(C(=O)C2=CC(=O)[N-]O2)CCC1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 99, 99, 99, 54, 28, 28, 28, 10, 1, 10, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 136, 136, 136, 136, 136, 99, 54, 54, 28, 28, 28, 1, 28, 28, 28, 28, 28, 28, 28, 28] 136 rigid atoms, others: [32, 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, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 533 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041989 none CCC(=O)NCC1CN(C(=O)C2=CC(=O)[N-]O2)CCC1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [74, 20, 20, 20, 6, 1, 1, 1, 1, 1, 7, 7, 28, 28, 28, 28, 28, 1, 1, 1, 1, 74, 74, 74, 74, 74, 20, 6, 6, 1, 1, 1, 28, 1, 1, 1, 1, 1, 2, 2, 2] 136 rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 17, 18, 19, 20, 37, 29, 30, 31] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 32, 38, 39, 40]) total number of confs: 309 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041989 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041989 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041989/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041989 Building REAL250005041990 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041990' /scratch/stefan/7921153/working/building/REAL250005041990 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041990 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041990/0 /scratch/stefan/7921153/working/building/REAL250005041990 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 99) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/99 `/scratch/stefan/7921153/working/3D/99' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC1CN(C(=O)C2=CC(=O)[N-]O2)CCC1C) `REAL250005041990.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041990.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041990/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041990 none CC(=O)NCC1CN(C(=O)C2=CC(=O)[N-]O2)CCC1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 34, 23, 23, 23, 10, 1, 10, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 49, 49, 49, 49, 34, 34, 23, 23, 23, 1, 23, 23, 23, 23, 23, 23, 23, 23] 49 rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 160 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041990 none CC(=O)NCC1CN(C(=O)C2=CC(=O)[N-]O2)CCC1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 4, 1, 1, 1, 1, 1, 7, 7, 23, 23, 23, 23, 23, 1, 1, 1, 1, 16, 16, 16, 16, 4, 4, 1, 1, 1, 23, 1, 1, 1, 1, 1, 2, 2, 2] 49 rigid atoms, others: [32, 33, 34, 4, 5, 6, 7, 8, 16, 17, 18, 19, 26, 27, 28, 30, 31] set([0, 1, 2, 3, 36, 37, 9, 10, 11, 12, 13, 14, 15, 35, 20, 21, 22, 23, 24, 25, 29]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041990 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041990 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041990/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041990 Building REAL250005041991 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041991' /scratch/stefan/7921153/working/building/REAL250005041991 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041991 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041991/0 /scratch/stefan/7921153/working/building/REAL250005041991 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 100) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/100 `/scratch/stefan/7921153/working/3D/100' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1CNC(=O)CO) `REAL250005041991.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041991.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041991/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041991 none CC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1CNC(=O)CO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 8, 1, 11, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 351 conformations in input total number of sets (complete confs): 351 using faster count positions algorithm for large data unique positions, atoms: [36, 36, 36, 36, 11, 1, 11, 1, 1, 1, 1, 1, 1, 36, 36, 36, 72, 117, 117, 117, 116, 36, 36, 36, 36, 36, 36, 36, 36, 1, 36, 36, 36, 72, 72, 117, 117, 117, 351] 351 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 736 number of broken/clashed sets: 15 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041991 none CC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1CNC(=O)CO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 8, 1, 11, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 351 conformations in input total number of sets (complete confs): 351 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 7, 36, 36, 36, 36, 36, 1, 1, 1, 6, 24, 24, 24, 56, 2, 2, 2, 1, 1, 1, 1, 1, 36, 1, 1, 1, 6, 6, 24, 58, 58, 174] 351 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 13, 14, 15, 24, 25, 26, 27, 28, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 29, 33, 34, 35, 36, 37, 38]) total number of confs: 437 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041991 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041991 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041991/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041991 Building REAL250005041992 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041992' /scratch/stefan/7921153/working/building/REAL250005041992 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041992 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041992/0 /scratch/stefan/7921153/working/building/REAL250005041992 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 101) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/101 `/scratch/stefan/7921153/working/3D/101' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(=O)NCC1CN(C(=O)C2=CC(=O)[N-]O2)CCC1C) `REAL250005041992.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041992/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041992 none C=CC(=O)NCC1CN(C(=O)C2=CC(=O)[N-]O2)CCC1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 92 conformations in input total number of sets (complete confs): 92 using faster count positions algorithm for large data unique positions, atoms: [92, 92, 92, 92, 45, 25, 25, 25, 10, 1, 10, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 92, 92, 92, 92, 45, 45, 25, 25, 25, 1, 25, 25, 25, 25, 25, 25, 25, 25] 92 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 289 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041992 none C=CC(=O)NCC1CN(C(=O)C2=CC(=O)[N-]O2)CCC1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 92 conformations in input total number of sets (complete confs): 92 using faster count positions algorithm for large data unique positions, atoms: [40, 18, 18, 18, 5, 1, 1, 1, 1, 1, 7, 7, 25, 25, 25, 25, 25, 1, 1, 1, 1, 40, 40, 40, 18, 5, 5, 1, 1, 1, 25, 1, 1, 1, 1, 1, 2, 2, 2] 92 rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 17, 18, 19, 20, 27, 28, 29, 31] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 30, 36, 37, 38]) total number of confs: 160 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041992 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041992 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041992/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041992 Building REAL250005041993 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041993' /scratch/stefan/7921153/working/building/REAL250005041993 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041993 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041993/0 /scratch/stefan/7921153/working/building/REAL250005041993 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 102) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/102 `/scratch/stefan/7921153/working/3D/102' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005041993.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041993/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041993 none CCC(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [197, 146, 146, 146, 115, 66, 117, 24, 8, 24, 8, 1, 8, 1, 1, 1, 1, 1, 1, 197, 197, 197, 197, 197, 146, 117, 117, 117, 117, 70, 70, 24, 24, 24, 24, 8, 1] 201 rigid atoms, others: [36, 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, 34, 35]) total number of confs: 911 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041993 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041993 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041993/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041993 Building REAL250005041994 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041994' /scratch/stefan/7921153/working/building/REAL250005041994 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041994 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041994/0 /scratch/stefan/7921153/working/building/REAL250005041994 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 103) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/103 `/scratch/stefan/7921153/working/3D/103' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005041994.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041994.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041994/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041994 none COCCC(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 176, 66, 66, 66, 41, 24, 42, 12, 4, 12, 4, 1, 4, 1, 1, 1, 1, 1, 1, 198, 198, 198, 198, 198, 176, 176, 66, 42, 42, 42, 42, 26, 26, 12, 12, 12, 12, 4, 1] 201 rigid atoms, others: [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, 36, 37, 38, 39]) total number of confs: 833 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041994 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041994 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041994/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041994 Building REAL250005041995 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041995' /scratch/stefan/7921153/working/building/REAL250005041995 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041995 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041995/0 /scratch/stefan/7921153/working/building/REAL250005041995 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 104) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/104 `/scratch/stefan/7921153/working/3D/104' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005041995.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041995.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041995/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041995 none CC(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 24, 18, 24, 14, 6, 14, 6, 1, 6, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24, 24, 24, 24, 18, 18, 14, 14, 14, 14, 6, 1] 24 rigid atoms, others: [33, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 103 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041995 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041995 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041995/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041995 Building REAL250005041996 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041996' /scratch/stefan/7921153/working/building/REAL250005041996 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041996 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041996/0 /scratch/stefan/7921153/working/building/REAL250005041996 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 105) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/105 `/scratch/stefan/7921153/working/3D/105' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC(C)NC(=O)C1CC1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005041996.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041996.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041996/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041996 none CC(CC(C)NC(=O)C1CC1)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', '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.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [19, 9, 19, 31, 41, 41, 53, 53, 53, 77, 77, 9, 1, 9, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 31, 31, 41, 41, 41, 41, 53, 77, 77, 77, 77, 77, 9, 1] 77 rigid atoms, others: [37, 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: 283 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041996 none CC(CC(C)NC(=O)C1CC1)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', '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.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [57, 46, 28, 11, 28, 11, 1, 11, 1, 1, 1, 57, 72, 72, 72, 77, 77, 77, 77, 77, 57, 57, 57, 57, 46, 46, 28, 28, 28, 28, 11, 1, 1, 1, 1, 1, 72, 77] 77 rigid atoms, others: [32, 33, 34, 35, 6, 8, 9, 10, 31] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37]) total number of confs: 309 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041996 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041996 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041996/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041996 Building REAL250005041997 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041997' /scratch/stefan/7921153/working/building/REAL250005041997 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041997 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041997/0 /scratch/stefan/7921153/working/building/REAL250005041997 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 106) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/106 `/scratch/stefan/7921153/working/3D/106' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC(C)NC(=O)C1CCC1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005041997.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041997.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041997/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041997 none CC(CC(C)NC(=O)C1CCC1)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', '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', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [16, 8, 16, 29, 41, 41, 49, 49, 49, 89, 89, 89, 8, 1, 8, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 29, 29, 41, 41, 41, 41, 49, 89, 89, 89, 89, 89, 89, 89, 8, 1] 89 rigid atoms, others: [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, 36, 37, 38, 39]) total number of confs: 329 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041997 none CC(CC(C)NC(=O)C1CCC1)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', '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', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [67, 52, 29, 9, 29, 9, 1, 9, 1, 1, 1, 1, 67, 84, 84, 84, 89, 89, 89, 89, 89, 67, 67, 67, 67, 52, 52, 29, 29, 29, 29, 9, 1, 1, 1, 1, 1, 1, 1, 84, 89] 89 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 38] 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, 29, 30, 31, 39, 40]) total number of confs: 375 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041997 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041997 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041997/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041997 Building REAL250005041998 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041998' /scratch/stefan/7921153/working/building/REAL250005041998 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041998 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041998/0 /scratch/stefan/7921153/working/building/REAL250005041998 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 107) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/107 `/scratch/stefan/7921153/working/3D/107' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC(C)NC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1CC1) `REAL250005041998.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041998.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041998/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041998 none CC(CC(C)NC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 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, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 69, 114, 166, 163, 198, 198, 198, 198, 198, 198, 198, 198, 24, 3, 24, 1, 1, 1, 1, 69, 69, 69, 69, 118, 118, 166, 166, 166, 166, 198, 198, 24, 3, 3, 1, 1, 1, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 40, 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]) total number of confs: 868 number of broken/clashed sets: 21 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041998 none CC(CC(C)NC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 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, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [58, 33, 13, 4, 13, 4, 1, 4, 1, 1, 1, 1, 1, 1, 57, 80, 80, 80, 157, 198, 198, 58, 58, 58, 58, 34, 34, 13, 13, 13, 13, 4, 1, 80, 157, 157, 198, 198, 198, 198, 198] 201 rigid atoms, others: [32, 6, 8, 9, 10, 11, 12, 13] 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, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 847 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041998 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041998 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041998/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041998 Building REAL250005041999 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005041999' /scratch/stefan/7921153/working/building/REAL250005041999 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005041999 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005041999/0 /scratch/stefan/7921153/working/building/REAL250005041999 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 108) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/108 `/scratch/stefan/7921153/working/3D/108' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005041999.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005041999.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005041999/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005041999 none COCC(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [97, 88, 56, 56, 56, 39, 24, 43, 13, 5, 13, 5, 1, 5, 1, 1, 1, 1, 1, 1, 97, 97, 97, 88, 88, 56, 43, 43, 43, 43, 29, 29, 13, 13, 13, 13, 5, 1] 101 rigid atoms, others: [37, 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: 442 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005041999 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005041999 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005041999/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005041999 Building REAL250005042000 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042000' /scratch/stefan/7921153/working/building/REAL250005042000 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042000 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042000/0 /scratch/stefan/7921153/working/building/REAL250005042000 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 109) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/109 `/scratch/stefan/7921153/working/3D/109' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005042000.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042000/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042000 none CCCC(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 187, 105, 105, 105, 73, 39, 74, 14, 4, 14, 4, 1, 4, 1, 1, 1, 1, 1, 1, 197, 197, 197, 197, 197, 187, 187, 105, 74, 74, 74, 74, 41, 41, 14, 14, 14, 14, 4, 1] 201 rigid atoms, others: [39, 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, 37, 38]) total number of confs: 872 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042000 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042000 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042000/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042000 Building REAL250005042001 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042001' /scratch/stefan/7921153/working/building/REAL250005042001 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042001 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042001/0 /scratch/stefan/7921153/working/building/REAL250005042001 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 110) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/110 `/scratch/stefan/7921153/working/3D/110' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005042001.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042001/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042001 none CC(C)CC(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 199, 199, 121, 121, 121, 78, 41, 79, 16, 6, 16, 6, 1, 6, 1, 1, 1, 1, 1, 1, 199, 199, 199, 199, 199, 199, 199, 199, 199, 121, 79, 79, 79, 79, 42, 42, 16, 16, 16, 16, 6, 1] 201 rigid atoms, others: [42, 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, 39, 40, 41]) total number of confs: 857 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042001 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042001 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042001/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042001 Building REAL250005042002 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042002' /scratch/stefan/7921153/working/building/REAL250005042002 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042002 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042002/0 /scratch/stefan/7921153/working/building/REAL250005042002 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 111) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/111 `/scratch/stefan/7921153/working/3D/111' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC(C)NC(=O)C1CC1C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005042002.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042002/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042002 none CC(CC(C)NC(=O)C1CC1C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', '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', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 27, 57, 84, 82, 114, 114, 114, 199, 199, 199, 10, 1, 10, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 59, 59, 84, 84, 84, 84, 114, 199, 199, 199, 199, 199, 199, 199, 10, 1] 201 rigid atoms, others: [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, 36, 37, 38, 39]) total number of confs: 718 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042002 none CC(CC(C)NC(=O)C1CC1C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', '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', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 86, 45, 12, 45, 12, 1, 12, 1, 1, 1, 1, 130, 184, 184, 184, 199, 199, 199, 199, 199, 131, 131, 131, 131, 88, 88, 45, 45, 45, 45, 12, 1, 1, 1, 1, 2, 2, 2, 184, 199] 201 rigid atoms, others: [32, 33, 34, 35, 6, 8, 9, 10, 11] 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, 29, 30, 31, 36, 37, 38, 39, 40]) total number of confs: 806 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042002 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042002 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042002/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042002 Building REAL250005042003 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042003' /scratch/stefan/7921153/working/building/REAL250005042003 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042003 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042003/0 /scratch/stefan/7921153/working/building/REAL250005042003 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 112) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/112 `/scratch/stefan/7921153/working/3D/112' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCC(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005042003.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042003.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042003/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042003 none CCOCC(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [178, 175, 151, 66, 66, 66, 41, 25, 43, 13, 4, 13, 4, 1, 4, 1, 1, 1, 1, 1, 1, 178, 178, 178, 178, 178, 151, 151, 66, 43, 43, 43, 43, 28, 28, 13, 13, 13, 13, 4, 1] 182 rigid atoms, others: [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, 36, 37, 38, 39]) total number of confs: 710 number of broken/clashed sets: 58 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042003 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042003 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042003/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042003 Building REAL250005042004 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042004' /scratch/stefan/7921153/working/building/REAL250005042004 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042004 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042004/0 /scratch/stefan/7921153/working/building/REAL250005042004 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 113) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/113 `/scratch/stefan/7921153/working/3D/113' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)=CC(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005042004.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042004.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042004/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042004 none CC(C)=CC(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 5, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 37, 37, 37, 29, 20, 29, 11, 4, 11, 4, 1, 4, 1, 1, 1, 1, 1, 1, 54, 54, 54, 54, 54, 54, 54, 37, 29, 29, 29, 29, 20, 20, 11, 11, 11, 11, 4, 1] 54 rigid atoms, others: [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, 36, 37, 38, 39]) total number of confs: 222 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042004 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042004 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042004/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042004 Building REAL250005042005 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042005' /scratch/stefan/7921153/working/building/REAL250005042005 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042005 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042005/0 /scratch/stefan/7921153/working/building/REAL250005042005 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 114) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/114 `/scratch/stefan/7921153/working/3D/114' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCC(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005042005.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042005.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042005/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042005 none CCCCC(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 195, 181, 65, 65, 65, 40, 21, 41, 9, 4, 9, 4, 1, 4, 1, 1, 1, 1, 1, 1, 194, 197, 197, 197, 197, 195, 195, 181, 181, 65, 41, 41, 41, 41, 22, 22, 9, 9, 9, 9, 4, 1] 201 rigid atoms, others: [42, 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, 39, 40, 41]) total number of confs: 828 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042005 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042005 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042005/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042005 Building REAL250005042006 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042006' /scratch/stefan/7921153/working/building/REAL250005042006 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042006 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042006/0 /scratch/stefan/7921153/working/building/REAL250005042006 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 115) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/115 `/scratch/stefan/7921153/working/3D/115' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005042006.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042006/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042006 none CC(C)C(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 90, 111, 90, 90, 70, 46, 70, 22, 10, 22, 10, 1, 10, 1, 1, 1, 1, 1, 1, 111, 111, 111, 111, 111, 111, 111, 90, 70, 70, 70, 70, 46, 46, 22, 22, 22, 22, 10, 1] 111 rigid atoms, others: [39, 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, 37, 38]) total number of confs: 497 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042006 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042006 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042006/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042006 Building REAL250005042007 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042007' /scratch/stefan/7921153/working/building/REAL250005042007 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042007 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042007/0 /scratch/stefan/7921153/working/building/REAL250005042007 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 116) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/116 `/scratch/stefan/7921153/working/3D/116' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)C(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005042007.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042007.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042007/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042007 none CCC(C)C(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 147, 83, 147, 83, 83, 57, 37, 57, 16, 7, 16, 7, 1, 7, 1, 1, 1, 1, 1, 1, 152, 152, 152, 152, 152, 147, 147, 147, 147, 83, 57, 57, 57, 57, 37, 37, 16, 16, 16, 16, 7, 1] 152 rigid atoms, others: [42, 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, 39, 40, 41]) total number of confs: 665 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042007 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042007 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042007/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042007 Building REAL250005042008 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042008' /scratch/stefan/7921153/working/building/REAL250005042008 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042008 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042008/0 /scratch/stefan/7921153/working/building/REAL250005042008 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 117) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/117 `/scratch/stefan/7921153/working/3D/117' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C)C(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005042008.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042008.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042008/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042008 none COC(C)C(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 39, 60, 39, 39, 25, 19, 25, 12, 5, 12, 5, 1, 5, 1, 1, 1, 1, 1, 1, 60, 60, 60, 60, 60, 60, 60, 39, 25, 25, 25, 25, 19, 19, 12, 12, 12, 12, 5, 1] 60 rigid atoms, others: [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, 36, 37, 38, 39]) total number of confs: 250 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042008 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042008 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042008/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042008 Building REAL250005042009 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042009' /scratch/stefan/7921153/working/building/REAL250005042009 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042009 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042009/0 /scratch/stefan/7921153/working/building/REAL250005042009 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 118) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/118 `/scratch/stefan/7921153/working/3D/118' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCCC(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005042009.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042009.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042009/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042009 none C=CCCC(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 174, 65, 65, 65, 42, 23, 43, 9, 4, 9, 4, 1, 4, 1, 1, 1, 1, 1, 1, 197, 197, 197, 197, 197, 174, 174, 65, 43, 43, 43, 43, 24, 24, 9, 9, 9, 9, 4, 1] 201 rigid atoms, others: [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, 36, 37, 38, 39]) total number of confs: 842 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042009 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042009 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042009/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042009 Building REAL250005042010 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042010' /scratch/stefan/7921153/working/building/REAL250005042010 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042010 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042010/0 /scratch/stefan/7921153/working/building/REAL250005042010 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 119) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/119 `/scratch/stefan/7921153/working/3D/119' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=C(C)C(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005042010.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042010.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042010/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042010 none CC=C(C)C(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 97 conformations in input total number of sets (complete confs): 97 using faster count positions algorithm for large data unique positions, atoms: [97, 97, 59, 97, 59, 59, 44, 28, 44, 18, 7, 18, 7, 1, 7, 1, 1, 1, 1, 1, 1, 97, 97, 97, 97, 97, 97, 97, 59, 44, 44, 44, 44, 28, 28, 18, 18, 18, 18, 7, 1] 97 rigid atoms, others: [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, 36, 37, 38, 39]) total number of confs: 365 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042010 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042010 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042010/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042010 Building REAL250005042011 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042011' /scratch/stefan/7921153/working/building/REAL250005042011 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042011 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042011/0 /scratch/stefan/7921153/working/building/REAL250005042011 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 120) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/120 `/scratch/stefan/7921153/working/3D/120' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC(C)NC(=O)C1(C)CC1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005042011.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042011.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042011/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042011 none CC(CC(C)NC(=O)C1(C)CC1)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', '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', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [20, 7, 20, 38, 55, 55, 81, 81, 81, 146, 146, 146, 7, 1, 7, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 39, 39, 55, 55, 55, 55, 81, 146, 146, 146, 146, 146, 146, 146, 7, 1] 146 rigid atoms, others: [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, 36, 37, 38, 39]) total number of confs: 568 number of broken/clashed sets: 13 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042011 none CC(CC(C)NC(=O)C1(C)CC1)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', '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', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [92, 58, 26, 7, 26, 7, 1, 7, 1, 1, 1, 1, 92, 133, 133, 133, 146, 146, 146, 146, 146, 92, 92, 92, 92, 58, 58, 26, 26, 26, 26, 7, 2, 2, 2, 1, 1, 1, 1, 133, 146] 146 rigid atoms, others: [35, 36, 37, 6, 8, 9, 10, 11, 38] 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, 29, 30, 31, 32, 33, 34, 39, 40]) total number of confs: 596 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042011 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042011 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042011/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042011 Building REAL250005042012 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042012' /scratch/stefan/7921153/working/building/REAL250005042012 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042012 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042012/0 /scratch/stefan/7921153/working/building/REAL250005042012 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 121) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/121 `/scratch/stefan/7921153/working/3D/121' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC(C)NC(=O)[C@@H]1C[C@H]1C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005042012.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042012.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042012/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042012 none CC(CC(C)NC(=O)[C@@H]1C[C@H]1C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 95 conformations in input total number of sets (complete confs): 95 using faster count positions algorithm for large data unique positions, atoms: [17, 6, 17, 35, 47, 47, 58, 58, 58, 95, 95, 95, 95, 95, 7, 1, 7, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 35, 35, 47, 47, 47, 47, 58, 95, 95, 95, 95, 95, 7, 1] 95 rigid atoms, others: [40, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 369 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042012 none CC(CC(C)NC(=O)[C@@H]1C[C@H]1C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 95 conformations in input total number of sets (complete confs): 95 using faster count positions algorithm for large data unique positions, atoms: [68, 57, 34, 11, 34, 11, 1, 11, 1, 1, 1, 1, 1, 1, 68, 90, 90, 90, 95, 95, 95, 95, 95, 68, 68, 68, 68, 57, 57, 34, 34, 34, 34, 11, 1, 1, 2, 2, 2, 90, 95] 95 rigid atoms, others: [34, 35, 6, 8, 9, 10, 11, 12, 13] 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, 36, 37, 38, 39, 40]) total number of confs: 399 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042012 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042012 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042012/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042012 Building REAL250005042013 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042013' /scratch/stefan/7921153/working/building/REAL250005042013 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042013 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042013/0 /scratch/stefan/7921153/working/building/REAL250005042013 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 122) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/122 `/scratch/stefan/7921153/working/3D/122' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC(C)NC(=O)[C@H]1C[C@@H]1C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005042013.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042013.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042013/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042013 none CC(CC(C)NC(=O)[C@H]1C[C@@H]1C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 10, 27, 57, 84, 82, 114, 114, 114, 199, 199, 199, 199, 199, 10, 1, 10, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 59, 59, 84, 84, 84, 84, 114, 199, 199, 199, 199, 199, 10, 1] 201 rigid atoms, others: [40, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 718 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042013 none CC(CC(C)NC(=O)[C@H]1C[C@@H]1C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [131, 86, 45, 12, 45, 12, 1, 12, 1, 1, 1, 1, 1, 1, 130, 184, 184, 184, 199, 199, 199, 199, 199, 131, 131, 131, 131, 88, 88, 45, 45, 45, 45, 12, 1, 1, 2, 2, 2, 184, 199] 201 rigid atoms, others: [34, 35, 6, 8, 9, 10, 11, 12, 13] 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, 36, 37, 38, 39, 40]) total number of confs: 806 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042013 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042013 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042013/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042013 Building REAL250005042014 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042014' /scratch/stefan/7921153/working/building/REAL250005042014 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042014 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042014/0 /scratch/stefan/7921153/working/building/REAL250005042014 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 123) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/123 `/scratch/stefan/7921153/working/3D/123' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC(C)NC(=O)C1=CC(=O)[N-]O1)NC(=O)C(N)=O) `REAL250005042014.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042014.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042014/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042014 none CC(CC(C)NC(=O)C1=CC(=O)[N-]O1)NC(=O)C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 52 conformations in input total number of sets (complete confs): 52 using faster count positions algorithm for large data unique positions, atoms: [43, 31, 17, 7, 17, 7, 1, 7, 1, 1, 1, 1, 1, 1, 43, 50, 50, 50, 52, 52, 43, 43, 43, 43, 32, 32, 17, 17, 17, 17, 7, 1, 50, 52, 52] 52 rigid atoms, others: [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, 32, 33, 34]) total number of confs: 219 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042014 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042014 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042014/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042014 Building REAL250005042015 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042015' /scratch/stefan/7921153/working/building/REAL250005042015 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042015 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042015/0 /scratch/stefan/7921153/working/building/REAL250005042015 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 124) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/124 `/scratch/stefan/7921153/working/3D/124' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC(C)NC(=O)C(C)(C)C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005042015.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042015.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042015/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042015 none CC(CC(C)NC(=O)C(C)(C)C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', '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', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [17, 7, 17, 28, 37, 37, 50, 50, 50, 55, 55, 55, 7, 1, 7, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 28, 28, 37, 37, 37, 37, 50, 55, 55, 55, 55, 55, 55, 55, 55, 55, 7, 1] 55 rigid atoms, others: [42, 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, 39, 40, 41]) total number of confs: 232 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042015 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042015 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042015/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042015 Building REAL250005042016 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042016' /scratch/stefan/7921153/working/building/REAL250005042016 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042016 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042016/0 /scratch/stefan/7921153/working/building/REAL250005042016 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 125) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/125 `/scratch/stefan/7921153/working/3D/125' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005042016.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042016.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042016/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042016 none C=CCC(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [200, 200, 102, 102, 102, 74, 45, 76, 15, 4, 15, 4, 1, 4, 1, 1, 1, 1, 1, 1, 200, 200, 200, 200, 200, 102, 76, 76, 76, 76, 49, 49, 15, 15, 15, 15, 4, 1] 201 rigid atoms, others: [37, 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: 880 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042016 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042016 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042016/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042016 Building REAL250005042017 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042017' /scratch/stefan/7921153/working/building/REAL250005042017 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005042017 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042017/0 /scratch/stefan/7921153/working/building/REAL250005042017 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 126) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/126 `/scratch/stefan/7921153/working/3D/126' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC(C)NC(=O)C1=CC(=O)[N-]O1)NC(=O)C[NH+](C)C) `REAL250005042017.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042017.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042017/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042017 none CC(CC(C)NC(=O)C1=CC(=O)[N-]O1)NC(=O)C[NH+](C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 3, 2, 3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 3, 3, 3, 3, 2, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4] 5 rigid atoms, others: [33, 6, 8, 9, 10, 11, 12, 13] 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, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 26 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042017 /scratch/stefan/7921153/working /scratch/stefan/7921153 mkdir: created directory `1' /scratch/stefan/7921153/working/building/REAL250005042017/1 /scratch/stefan/7921153/working/building/REAL250005042017 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 1 (index: 127) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/127 `/scratch/stefan/7921153/working/3D/127' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC(C)NC(=O)C1=CC(=O)[N-]O1)NC(=O)CN(C)C) `REAL250005042017.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005042017.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042017/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.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: REAL250005042017 none CC(CC(C)NC(=O)C1=CC(=O)[N-]O1)NC(=O)CN(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 132 conformations in input total number of sets (complete confs): 132 using faster count positions algorithm for large data unique positions, atoms: [45, 27, 15, 5, 15, 5, 1, 5, 1, 1, 1, 1, 1, 1, 41, 63, 63, 63, 125, 129, 129, 45, 45, 45, 45, 32, 32, 15, 15, 15, 15, 5, 1, 63, 125, 125, 129, 129, 129, 129, 129, 129] 132 rigid atoms, others: [32, 6, 8, 9, 10, 11, 12, 13] 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, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 576 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042017 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042017 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 1: /scratch/stefan/7921153/working/building/REAL250005042017/1.* 0: /scratch/stefan/7921153/working/building/REAL250005042017/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042017 Building REAL250005042018 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042018' /scratch/stefan/7921153/working/building/REAL250005042018 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042018 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042018/0 /scratch/stefan/7921153/working/building/REAL250005042018 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 128) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/128 `/scratch/stefan/7921153/working/3D/128' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(O)C(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005042018.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042018/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042018 none C=CC(O)C(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [37, 36, 24, 36, 24, 24, 18, 13, 19, 9, 3, 9, 3, 1, 3, 1, 1, 1, 1, 1, 1, 37, 37, 37, 36, 108, 24, 19, 19, 19, 19, 15, 15, 9, 9, 9, 9, 3, 1] 111 rigid atoms, others: [38, 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]) total number of confs: 287 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042018 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042018 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042018/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042018 Building REAL250005042019 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042019' /scratch/stefan/7921153/working/building/REAL250005042019 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042019 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042019/0 /scratch/stefan/7921153/working/building/REAL250005042019 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 129) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/129 `/scratch/stefan/7921153/working/3D/129' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC(C)NC(=O)C1COC1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005042019.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042019.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042019/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042019 none CC(CC(C)NC(=O)C1COC1)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 165 conformations in input total number of sets (complete confs): 165 using faster count positions algorithm for large data unique positions, atoms: [25, 10, 25, 51, 73, 73, 103, 103, 103, 165, 165, 165, 10, 1, 10, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 52, 52, 73, 73, 73, 73, 103, 165, 165, 165, 165, 165, 10, 1] 165 rigid atoms, others: [38, 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]) total number of confs: 626 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042019 none CC(CC(C)NC(=O)C1COC1)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 165 conformations in input total number of sets (complete confs): 165 using faster count positions algorithm for large data unique positions, atoms: [110, 74, 37, 11, 37, 11, 1, 11, 1, 1, 1, 1, 110, 153, 153, 153, 165, 165, 165, 165, 165, 110, 110, 110, 110, 76, 76, 37, 37, 37, 37, 11, 1, 1, 1, 1, 1, 153, 165] 165 rigid atoms, others: [32, 33, 34, 35, 36, 6, 8, 9, 10, 11] 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, 29, 30, 31, 37, 38]) total number of confs: 670 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042019 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042019 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042019/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042019 Building REAL250005042020 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042020' /scratch/stefan/7921153/working/building/REAL250005042020 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042020 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042020/0 /scratch/stefan/7921153/working/building/REAL250005042020 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 130) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/130 `/scratch/stefan/7921153/working/3D/130' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H](C)C(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005042020.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042020/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042020 none CO[C@H](C)C(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [67, 66, 40, 66, 66, 40, 40, 32, 22, 33, 12, 4, 12, 4, 1, 4, 1, 1, 1, 1, 1, 1, 67, 67, 67, 66, 66, 66, 40, 33, 33, 33, 33, 24, 24, 12, 12, 12, 12, 4, 1] 68 rigid atoms, others: [40, 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]) total number of confs: 300 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042020 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042020 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042020/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042020 Building REAL250005042021 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042021' /scratch/stefan/7921153/working/building/REAL250005042021 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042021 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042021/0 /scratch/stefan/7921153/working/building/REAL250005042021 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 131) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/131 `/scratch/stefan/7921153/working/3D/131' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC=CC(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005042021.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042021/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042021 none CCC=CC(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 156, 156, 100, 100, 100, 67, 36, 68, 13, 4, 13, 4, 1, 4, 1, 1, 1, 1, 1, 1, 198, 198, 198, 198, 198, 156, 156, 100, 68, 68, 68, 68, 37, 37, 13, 13, 13, 13, 4, 1] 201 rigid atoms, others: [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, 36, 37, 38, 39]) total number of confs: 854 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042021 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042021 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042021/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042021 Building REAL250005042022 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042022' /scratch/stefan/7921153/working/building/REAL250005042022 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types Protomer extracton resulted in 0 protomers Marking REAL250005042022 as failed and skipping /scratch/stefan/7921153/working /scratch/stefan/7921153 mkdir: created directory `/scratch/stefan/7921153/failed' `/scratch/stefan/7921153/working/building/REAL250005042022' -> `/scratch/stefan/7921153/failed/REAL250005042022' Building REAL250005042023 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042023' /scratch/stefan/7921153/working/building/REAL250005042023 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042023 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042023/0 /scratch/stefan/7921153/working/building/REAL250005042023 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 132) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/132 `/scratch/stefan/7921153/working/3D/132' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC(C)NC(=O)C1=CC(=O)[N-]O1)NC(=O)CO) `REAL250005042023.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042023.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042023/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042023 none CC(CC(C)NC(=O)C1=CC(=O)[N-]O1)NC(=O)CO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [32, 23, 16, 6, 16, 6, 1, 6, 1, 1, 1, 1, 1, 1, 30, 41, 41, 41, 50, 32, 32, 32, 32, 26, 26, 16, 16, 16, 16, 6, 1, 41, 50, 50, 150] 159 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 30] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34]) total number of confs: 387 number of broken/clashed sets: 54 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042023 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042023 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042023/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042023 Building REAL250005042024 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042024' /scratch/stefan/7921153/working/building/REAL250005042024 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042024 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042024/0 /scratch/stefan/7921153/working/building/REAL250005042024 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 133) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/133 `/scratch/stefan/7921153/working/3D/133' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)C(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005042024.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042024/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042024 none CC(O)C(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [47, 33, 47, 33, 33, 26, 19, 26, 11, 4, 11, 4, 1, 4, 1, 1, 1, 1, 1, 1, 47, 47, 47, 47, 141, 33, 26, 26, 26, 26, 19, 19, 11, 11, 11, 11, 4, 1] 141 rigid atoms, others: [37, 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: 358 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042024 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042024 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042024/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042024 Building REAL250005042025 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042025' /scratch/stefan/7921153/working/building/REAL250005042025 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042025 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042025/0 /scratch/stefan/7921153/working/building/REAL250005042025 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 134) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/134 `/scratch/stefan/7921153/working/3D/134' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC(C)NC(=O)C1CC1F)NC(=O)C1=CC(=O)[N-]O1) `REAL250005042025.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042025.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042025/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042025 none CC(CC(C)NC(=O)C1CC1F)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 15, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [27, 10, 27, 59, 83, 83, 109, 109, 109, 176, 176, 176, 10, 1, 10, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 60, 60, 83, 83, 83, 83, 109, 176, 176, 176, 176, 10, 1] 176 rigid atoms, others: [37, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 660 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042025 none CC(CC(C)NC(=O)C1CC1F)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 15, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [121, 80, 39, 13, 39, 13, 1, 13, 1, 1, 1, 1, 121, 162, 162, 162, 176, 176, 176, 176, 176, 121, 121, 121, 121, 83, 83, 39, 39, 39, 39, 13, 1, 1, 1, 1, 162, 176] 176 rigid atoms, others: [32, 33, 34, 35, 6, 8, 9, 10, 11] 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, 29, 30, 31, 36, 37]) total number of confs: 732 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042025 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042025 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042025/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042025 Building REAL250005042026 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042026' /scratch/stefan/7921153/working/building/REAL250005042026 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042026 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042026/0 /scratch/stefan/7921153/working/building/REAL250005042026 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 135) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/135 `/scratch/stefan/7921153/working/3D/135' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC(C)NC(=O)C1=CC(=O)[N-]O1)NC(=O)CCF) `REAL250005042026.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042026/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042026 none CC(CC(C)NC(=O)C1=CC(=O)[N-]O1)NC(=O)CCF NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [66, 34, 14, 4, 14, 4, 1, 4, 1, 1, 1, 1, 1, 1, 65, 98, 98, 98, 198, 198, 66, 66, 66, 66, 37, 37, 14, 14, 14, 14, 4, 1, 98, 198, 198, 198, 198] 201 rigid atoms, others: [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, 32, 33, 34, 35, 36]) total number of confs: 813 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042026 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042026 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042026/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042026 Building REAL250005042027 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042027' /scratch/stefan/7921153/working/building/REAL250005042027 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042027 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042027/0 /scratch/stefan/7921153/working/building/REAL250005042027 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 136) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/136 `/scratch/stefan/7921153/working/3D/136' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC(C)NC(=O)C1=CC(=O)[N-]O1)NC(=O)C=CCF) `REAL250005042027.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042027.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042027/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042027 none CC(CC(C)NC(=O)C1=CC(=O)[N-]O1)NC(=O)C=CCF NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 5, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 156 conformations in input total number of sets (complete confs): 156 using faster count positions algorithm for large data unique positions, atoms: [50, 27, 13, 4, 13, 4, 1, 4, 1, 1, 1, 1, 1, 1, 49, 77, 77, 77, 143, 143, 153, 50, 50, 50, 50, 28, 28, 13, 13, 13, 13, 4, 1, 77, 143, 143, 153, 153] 156 rigid atoms, others: [32, 6, 8, 9, 10, 11, 12, 13] 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, 33, 34, 35, 36, 37]) total number of confs: 583 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042027 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042027 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042027/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042027 Building REAL250005042028 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042028' /scratch/stefan/7921153/working/building/REAL250005042028 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042028 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042028/0 /scratch/stefan/7921153/working/building/REAL250005042028 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 137) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/137 `/scratch/stefan/7921153/working/3D/137' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCC(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005042028.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042028/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042028 none C#CCCC(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [198, 198, 182, 83, 83, 83, 59, 35, 60, 14, 4, 14, 4, 1, 4, 1, 1, 1, 1, 1, 1, 198, 198, 198, 182, 182, 83, 60, 60, 60, 60, 36, 36, 14, 14, 14, 14, 4, 1] 201 rigid atoms, others: [38, 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]) total number of confs: 857 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042028 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042028 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042028/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042028 Building REAL250005042029 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042029' /scratch/stefan/7921153/working/building/REAL250005042029 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042029 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042029/0 /scratch/stefan/7921153/working/building/REAL250005042029 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 138) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/138 `/scratch/stefan/7921153/working/3D/138' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC(C)NC(=O)C1CCO1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005042029.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042029.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042029/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042029 none CC(CC(C)NC(=O)C1CCO1)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 12, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [19, 8, 19, 34, 50, 50, 55, 55, 55, 59, 59, 59, 8, 1, 8, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 35, 35, 50, 50, 50, 50, 55, 59, 59, 59, 59, 59, 8, 1] 59 rigid atoms, others: [38, 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]) total number of confs: 251 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042029 none CC(CC(C)NC(=O)C1CCO1)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 12, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [41, 29, 18, 7, 18, 7, 1, 7, 1, 1, 1, 1, 41, 55, 55, 55, 59, 59, 59, 59, 59, 41, 41, 41, 41, 29, 29, 18, 18, 18, 18, 7, 1, 1, 1, 1, 1, 55, 59] 59 rigid atoms, others: [32, 33, 34, 35, 36, 6, 8, 9, 10, 11] 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, 29, 30, 31, 37, 38]) total number of confs: 237 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042029 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042029 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042029/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042029 Building REAL250005042030 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042030' /scratch/stefan/7921153/working/building/REAL250005042030 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042030 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042030/0 /scratch/stefan/7921153/working/building/REAL250005042030 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 139) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/139 `/scratch/stefan/7921153/working/3D/139' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC(C)NC(=O)C(C)(C)O)NC(=O)C1=CC(=O)[N-]O1) `REAL250005042030.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042030/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042030 none CC(CC(C)NC(=O)C(C)(C)O)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 12, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 240 conformations in input total number of sets (complete confs): 240 using faster count positions algorithm for large data unique positions, atoms: [24, 10, 24, 37, 49, 49, 61, 61, 61, 80, 80, 80, 10, 1, 10, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 37, 37, 49, 49, 49, 49, 61, 80, 80, 80, 80, 80, 80, 240, 10, 1] 240 rigid atoms, others: [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, 36, 37, 38, 39]) total number of confs: 599 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042030 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042030 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042030/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042030 Building REAL250005042031 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042031' /scratch/stefan/7921153/working/building/REAL250005042031 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042031 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042031/0 /scratch/stefan/7921153/working/building/REAL250005042031 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 140) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/140 `/scratch/stefan/7921153/working/3D/140' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC1C(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005042031.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042031.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042031/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042031 none CC1=CC1C(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 156 conformations in input total number of sets (complete confs): 156 using faster count positions algorithm for large data unique positions, atoms: [156, 156, 156, 90, 90, 90, 67, 45, 67, 21, 8, 21, 8, 1, 8, 1, 1, 1, 1, 1, 1, 156, 156, 156, 156, 156, 90, 67, 67, 67, 67, 45, 45, 21, 21, 21, 21, 8, 1] 156 rigid atoms, others: [38, 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]) total number of confs: 559 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042031 none CC1=CC1C(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 156 conformations in input total number of sets (complete confs): 156 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 13, 13, 13, 51, 51, 90, 127, 127, 151, 151, 151, 156, 156, 156, 156, 156, 2, 2, 2, 1, 1, 13, 51, 51, 51, 51, 93, 93, 127, 127, 127, 127, 151, 156] 156 rigid atoms, others: [0, 1, 2, 3, 4, 24, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 692 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042031 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042031 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042031/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042031 Building REAL250005042032 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042032' /scratch/stefan/7921153/working/building/REAL250005042032 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042032 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042032/0 /scratch/stefan/7921153/working/building/REAL250005042032 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 141) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/141 `/scratch/stefan/7921153/working/3D/141' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC(C)NC(=O)[C@@H](C)O)NC(=O)C1=CC(=O)[N-]O1) `REAL250005042032.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042032/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042032 none CC(CC(C)NC(=O)[C@@H](C)O)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 12, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 282 conformations in input total number of sets (complete confs): 282 using faster count positions algorithm for large data unique positions, atoms: [22, 10, 22, 41, 61, 60, 79, 79, 79, 94, 94, 94, 10, 1, 10, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 42, 42, 61, 61, 61, 61, 79, 94, 94, 94, 282, 10, 1] 282 rigid atoms, others: [37, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 689 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042032 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042032 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042032/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042032 Building REAL250005042033 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042033' /scratch/stefan/7921153/working/building/REAL250005042033 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042033 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042033/0 /scratch/stefan/7921153/working/building/REAL250005042033 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 142) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/142 `/scratch/stefan/7921153/working/3D/142' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC(C)NC(=O)C1=CC(=O)[N-]O1)NC(=O)C=CCO) `REAL250005042033.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042033.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042033/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042033 none CC(CC(C)NC(=O)C1=CC(=O)[N-]O1)NC(=O)C=CCO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [63, 34, 14, 4, 14, 4, 1, 4, 1, 1, 1, 1, 1, 1, 62, 97, 97, 97, 183, 183, 198, 63, 63, 63, 63, 35, 35, 14, 14, 14, 14, 4, 1, 97, 183, 183, 198, 198, 594] 603 rigid atoms, others: [32, 6, 8, 9, 10, 11, 12, 13] 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, 33, 34, 35, 36, 37, 38]) total number of confs: 1344 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042033 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042033 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042033/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042033 Building REAL250005042034 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042034' /scratch/stefan/7921153/working/building/REAL250005042034 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042034 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042034/0 /scratch/stefan/7921153/working/building/REAL250005042034 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 143) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/143 `/scratch/stefan/7921153/working/3D/143' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC(C)NC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CCC1) `REAL250005042034.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042034.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042034/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042034 none CC(CC(C)NC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 5, 5, 7, 7, 7, 7, 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, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [13, 7, 13, 21, 29, 29, 37, 37, 37, 38, 38, 38, 38, 38, 7, 1, 7, 1, 1, 1, 1, 13, 13, 13, 13, 22, 22, 29, 29, 29, 29, 37, 38, 7, 1, 1, 1, 1, 1] 38 rigid atoms, others: [34, 35, 36, 37, 38, 15, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 148 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042034 none CC(CC(C)NC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 5, 5, 7, 7, 7, 7, 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, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [33, 23, 12, 5, 12, 5, 1, 5, 1, 1, 1, 1, 1, 1, 33, 38, 38, 38, 38, 38, 38, 33, 33, 33, 33, 23, 23, 12, 12, 12, 12, 5, 1, 38, 38, 38, 38, 38, 38] 38 rigid atoms, others: [32, 6, 8, 9, 10, 11, 12, 13] 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, 33, 34, 35, 36, 37, 38]) total number of confs: 163 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042034 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042034 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042034/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042034 Building REAL250005042035 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042035' /scratch/stefan/7921153/working/building/REAL250005042035 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042035 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042035/0 /scratch/stefan/7921153/working/building/REAL250005042035 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 144) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/144 `/scratch/stefan/7921153/working/3D/144' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CON=CC(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005042035.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042035.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042035/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042035 none CON=CC(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [47, 47, 47, 27, 27, 27, 20, 15, 22, 10, 4, 10, 4, 1, 4, 1, 1, 1, 1, 1, 1, 47, 47, 47, 47, 27, 22, 22, 22, 22, 18, 18, 10, 10, 10, 10, 4, 1] 48 rigid atoms, others: [37, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 189 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042035 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042035 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042035/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042035 Building REAL250005042036 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042036' /scratch/stefan/7921153/working/building/REAL250005042036 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042036 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042036/0 /scratch/stefan/7921153/working/building/REAL250005042036 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 145) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/145 `/scratch/stefan/7921153/working/3D/145' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC(C)NC(=O)C1(F)CC1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005042036.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042036/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042036 none CC(CC(C)NC(=O)C1(F)CC1)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 15, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [24, 9, 24, 46, 70, 69, 104, 104, 104, 153, 153, 153, 9, 1, 9, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 47, 47, 70, 70, 70, 70, 104, 153, 153, 153, 153, 9, 1] 154 rigid atoms, others: [37, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 577 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042036 none CC(CC(C)NC(=O)C1(F)CC1)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 15, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [104, 68, 34, 11, 34, 11, 1, 11, 1, 1, 1, 1, 103, 145, 145, 145, 153, 153, 153, 153, 153, 104, 104, 104, 104, 71, 71, 34, 34, 34, 34, 11, 1, 1, 1, 1, 145, 153] 154 rigid atoms, others: [32, 33, 34, 35, 6, 8, 9, 10, 11] 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, 29, 30, 31, 36, 37]) total number of confs: 626 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042036 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042036 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042036/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042036 Building REAL250005042037 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042037' /scratch/stefan/7921153/working/building/REAL250005042037 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042037 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042037/0 /scratch/stefan/7921153/working/building/REAL250005042037 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 146) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/146 `/scratch/stefan/7921153/working/3D/146' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=C(F)C(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005042037.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042037/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042037 none CC=C(F)C(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 15, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [118, 118, 77, 118, 77, 77, 57, 31, 58, 12, 4, 12, 4, 1, 4, 1, 1, 1, 1, 1, 1, 118, 118, 118, 118, 77, 58, 58, 58, 58, 33, 33, 12, 12, 12, 12, 4, 1] 119 rigid atoms, others: [37, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 467 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042037 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042037 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042037/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042037 Building REAL250005042038 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042038' /scratch/stefan/7921153/working/building/REAL250005042038 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042038 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042038/0 /scratch/stefan/7921153/working/building/REAL250005042038 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 147) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/147 `/scratch/stefan/7921153/working/3D/147' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC(C)NC(=O)C(C)CO)NC(=O)C1=CC(=O)[N-]O1) `REAL250005042038.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042038/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042038 none CC(CC(C)NC(=O)C(C)CO)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 12, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [6, 4, 6, 8, 10, 10, 14, 14, 14, 20, 20, 20, 4, 1, 4, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 8, 8, 10, 10, 10, 10, 14, 20, 20, 20, 20, 20, 20, 60, 4, 1] 60 rigid atoms, others: [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, 36, 37, 38, 39]) total number of confs: 146 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042038 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042038 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042038/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042038 Building REAL250005042039 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042039' /scratch/stefan/7921153/working/building/REAL250005042039 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042039 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042039/0 /scratch/stefan/7921153/working/building/REAL250005042039 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 148) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/148 `/scratch/stefan/7921153/working/3D/148' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC(C)NC(=O)[C@H](C)O)NC(=O)C1=CC(=O)[N-]O1) `REAL250005042039.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042039/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042039 none CC(CC(C)NC(=O)[C@H](C)O)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 12, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [21, 8, 21, 34, 43, 43, 54, 54, 54, 58, 58, 58, 8, 1, 8, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 34, 34, 43, 43, 43, 43, 54, 58, 58, 58, 174, 8, 1] 174 rigid atoms, others: [37, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 415 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042039 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042039 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042039/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042039 Building REAL250005042040 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042040' /scratch/stefan/7921153/working/building/REAL250005042040 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042040 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042040/0 /scratch/stefan/7921153/working/building/REAL250005042040 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 149) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/149 `/scratch/stefan/7921153/working/3D/149' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C1CC1C(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005042040.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042040.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042040/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042040 none C=C1CC1C(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 82, 82, 82, 66, 42, 66, 19, 6, 19, 6, 1, 6, 1, 1, 1, 1, 1, 1, 142, 142, 142, 142, 142, 82, 66, 66, 66, 66, 42, 42, 19, 19, 19, 19, 6, 1] 142 rigid atoms, others: [38, 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]) total number of confs: 528 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042040 none C=C1CC1C(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 142 conformations in input total number of sets (complete confs): 142 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 13, 13, 13, 51, 51, 86, 119, 119, 139, 139, 139, 142, 142, 142, 142, 142, 1, 1, 1, 1, 1, 13, 51, 51, 51, 51, 89, 89, 119, 119, 119, 119, 139, 142] 142 rigid atoms, others: [0, 1, 2, 3, 4, 21, 22, 23, 24, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 606 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042040 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042040 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042040/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042040 Building REAL250005042041 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042041' /scratch/stefan/7921153/working/building/REAL250005042041 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042041 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042041/0 /scratch/stefan/7921153/working/building/REAL250005042041 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 150) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/150 `/scratch/stefan/7921153/working/3D/150' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C(C)CC(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005042041.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042041/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042041 none C=C(C)CC(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 99, 99, 99, 66, 40, 67, 15, 4, 15, 4, 1, 4, 1, 1, 1, 1, 1, 1, 199, 199, 199, 199, 199, 199, 199, 99, 67, 67, 67, 67, 42, 42, 15, 15, 15, 15, 4, 1] 201 rigid atoms, others: [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, 36, 37, 38, 39]) total number of confs: 832 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042041 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042041 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042041/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042041 Building REAL250005042042 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042042' /scratch/stefan/7921153/working/building/REAL250005042042 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042042 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042042/0 /scratch/stefan/7921153/working/building/REAL250005042042 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 151) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/151 `/scratch/stefan/7921153/working/3D/151' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=CC(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005042042.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042042.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042042/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042042 none CC=CC(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 124 conformations in input total number of sets (complete confs): 124 using faster count positions algorithm for large data unique positions, atoms: [122, 122, 96, 96, 96, 70, 42, 72, 19, 7, 19, 7, 1, 7, 1, 1, 1, 1, 1, 1, 122, 122, 122, 122, 122, 96, 72, 72, 72, 72, 44, 44, 19, 19, 19, 19, 7, 1] 124 rigid atoms, others: [37, 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: 516 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042042 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042042 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042042/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042042 Building REAL250005042043 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042043' /scratch/stefan/7921153/working/building/REAL250005042043 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042043 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042043/0 /scratch/stefan/7921153/working/building/REAL250005042043 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 152) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/152 `/scratch/stefan/7921153/working/3D/152' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC(C)NC(=O)[C@@H]1C[C@H]1C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005042043.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042043.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042043/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042043 none CC(CC(C)NC(=O)[C@@H]1C[C@H]1C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 95 conformations in input total number of sets (complete confs): 95 using faster count positions algorithm for large data unique positions, atoms: [17, 6, 17, 35, 47, 47, 58, 58, 58, 95, 95, 95, 95, 95, 7, 1, 7, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 35, 35, 47, 47, 47, 47, 58, 95, 95, 95, 95, 95, 7, 1] 95 rigid atoms, others: [40, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 369 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042043 none CC(CC(C)NC(=O)[C@@H]1C[C@H]1C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 95 conformations in input total number of sets (complete confs): 95 using faster count positions algorithm for large data unique positions, atoms: [68, 57, 34, 11, 34, 11, 1, 11, 1, 1, 1, 1, 1, 1, 68, 90, 90, 90, 95, 95, 95, 95, 95, 68, 68, 68, 68, 57, 57, 34, 34, 34, 34, 11, 1, 1, 2, 2, 2, 90, 95] 95 rigid atoms, others: [34, 35, 6, 8, 9, 10, 11, 12, 13] 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, 36, 37, 38, 39, 40]) total number of confs: 399 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042043 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042043 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042043/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042043 Building REAL250005042044 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042044' /scratch/stefan/7921153/working/building/REAL250005042044 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042044 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042044/0 /scratch/stefan/7921153/working/building/REAL250005042044 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 153) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/153 `/scratch/stefan/7921153/working/3D/153' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC(C)NC(=O)C1(O)CC1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005042044.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042044.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042044/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042044 none CC(CC(C)NC(=O)C1(O)CC1)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 228 conformations in input total number of sets (complete confs): 228 using faster count positions algorithm for large data unique positions, atoms: [20, 7, 20, 36, 49, 49, 64, 64, 64, 76, 76, 76, 7, 1, 7, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 36, 36, 49, 49, 49, 49, 64, 228, 76, 76, 76, 76, 7, 1] 228 rigid atoms, others: [38, 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]) total number of confs: 542 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042044 none CC(CC(C)NC(=O)C1(O)CC1)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 228 conformations in input total number of sets (complete confs): 228 using faster count positions algorithm for large data unique positions, atoms: [58, 45, 27, 11, 27, 11, 1, 11, 1, 1, 1, 1, 58, 72, 72, 72, 76, 76, 76, 76, 76, 58, 58, 58, 58, 45, 45, 27, 27, 27, 27, 11, 6, 1, 1, 1, 1, 72, 76] 228 rigid atoms, others: [33, 34, 35, 36, 6, 8, 9, 10, 11] 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, 29, 30, 31, 32, 37, 38]) total number of confs: 318 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042044 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042044 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042044/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042044 Building REAL250005042045 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042045' /scratch/stefan/7921153/working/building/REAL250005042045 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042045 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042045/0 /scratch/stefan/7921153/working/building/REAL250005042045 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 154) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/154 `/scratch/stefan/7921153/working/3D/154' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC(C)NC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1CC1) `REAL250005042045.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042045.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042045/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042045 none CC(CC(C)NC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 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, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 69, 114, 166, 163, 198, 198, 198, 198, 198, 198, 198, 198, 24, 3, 24, 1, 1, 1, 1, 69, 69, 69, 69, 118, 118, 166, 166, 166, 166, 198, 198, 24, 3, 3, 1, 1, 1, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 40, 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]) total number of confs: 868 number of broken/clashed sets: 21 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042045 none CC(CC(C)NC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 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, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [58, 33, 13, 4, 13, 4, 1, 4, 1, 1, 1, 1, 1, 1, 57, 80, 80, 80, 157, 198, 198, 58, 58, 58, 58, 34, 34, 13, 13, 13, 13, 4, 1, 80, 157, 157, 198, 198, 198, 198, 198] 201 rigid atoms, others: [32, 6, 8, 9, 10, 11, 12, 13] 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, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 847 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042045 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042045 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042045/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042045 Building REAL250005042046 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042046' /scratch/stefan/7921153/working/building/REAL250005042046 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042046 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042046/0 /scratch/stefan/7921153/working/building/REAL250005042046 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 155) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/155 `/scratch/stefan/7921153/working/3D/155' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005042046.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042046.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042046/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042046 none COCC(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [97, 88, 56, 56, 56, 39, 24, 43, 13, 5, 13, 5, 1, 5, 1, 1, 1, 1, 1, 1, 97, 97, 97, 88, 88, 56, 43, 43, 43, 43, 29, 29, 13, 13, 13, 13, 5, 1] 101 rigid atoms, others: [37, 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: 442 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042046 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042046 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042046/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042046 Building REAL250005042047 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042047' /scratch/stefan/7921153/working/building/REAL250005042047 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042047 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042047/0 /scratch/stefan/7921153/working/building/REAL250005042047 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 156) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/156 `/scratch/stefan/7921153/working/3D/156' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005042047.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042047.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042047/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042047 none CCCC(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 187, 105, 105, 105, 73, 39, 74, 14, 4, 14, 4, 1, 4, 1, 1, 1, 1, 1, 1, 197, 197, 197, 197, 197, 187, 187, 105, 74, 74, 74, 74, 41, 41, 14, 14, 14, 14, 4, 1] 201 rigid atoms, others: [39, 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, 37, 38]) total number of confs: 872 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042047 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042047 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042047/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042047 Building REAL250005042048 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042048' /scratch/stefan/7921153/working/building/REAL250005042048 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042048 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042048/0 /scratch/stefan/7921153/working/building/REAL250005042048 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 157) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/157 `/scratch/stefan/7921153/working/3D/157' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005042048.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042048.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042048/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042048 none CC(C)CC(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 199, 199, 121, 121, 121, 78, 41, 79, 16, 6, 16, 6, 1, 6, 1, 1, 1, 1, 1, 1, 199, 199, 199, 199, 199, 199, 199, 199, 199, 121, 79, 79, 79, 79, 42, 42, 16, 16, 16, 16, 6, 1] 201 rigid atoms, others: [42, 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, 39, 40, 41]) total number of confs: 857 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042048 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042048 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042048/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042048 Building REAL250005042049 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042049' /scratch/stefan/7921153/working/building/REAL250005042049 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042049 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042049/0 /scratch/stefan/7921153/working/building/REAL250005042049 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 158) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/158 `/scratch/stefan/7921153/working/3D/158' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC(C)NC(=O)C1CC1C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005042049.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042049/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042049 none CC(CC(C)NC(=O)C1CC1C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', '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', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 27, 57, 84, 82, 114, 114, 114, 199, 199, 199, 10, 1, 10, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 59, 59, 84, 84, 84, 84, 114, 199, 199, 199, 199, 199, 199, 199, 10, 1] 201 rigid atoms, others: [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, 36, 37, 38, 39]) total number of confs: 718 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042049 none CC(CC(C)NC(=O)C1CC1C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', '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', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 86, 45, 12, 45, 12, 1, 12, 1, 1, 1, 1, 130, 184, 184, 184, 199, 199, 199, 199, 199, 131, 131, 131, 131, 88, 88, 45, 45, 45, 45, 12, 1, 1, 1, 1, 2, 2, 2, 184, 199] 201 rigid atoms, others: [32, 33, 34, 35, 6, 8, 9, 10, 11] 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, 29, 30, 31, 36, 37, 38, 39, 40]) total number of confs: 806 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042049 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042049 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042049/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042049 Building REAL250005042050 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042050' /scratch/stefan/7921153/working/building/REAL250005042050 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042050 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042050/0 /scratch/stefan/7921153/working/building/REAL250005042050 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 159) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/159 `/scratch/stefan/7921153/working/3D/159' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCC(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005042050.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042050.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042050/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042050 none CCOCC(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [178, 175, 151, 66, 66, 66, 41, 25, 43, 13, 4, 13, 4, 1, 4, 1, 1, 1, 1, 1, 1, 178, 178, 178, 178, 178, 151, 151, 66, 43, 43, 43, 43, 28, 28, 13, 13, 13, 13, 4, 1] 182 rigid atoms, others: [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, 36, 37, 38, 39]) total number of confs: 710 number of broken/clashed sets: 58 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042050 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042050 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042050/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042050 Building REAL250005042051 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042051' /scratch/stefan/7921153/working/building/REAL250005042051 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042051 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042051/0 /scratch/stefan/7921153/working/building/REAL250005042051 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 160) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/160 `/scratch/stefan/7921153/working/3D/160' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)=CC(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005042051.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042051/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042051 none CC(C)=CC(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 5, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 37, 37, 37, 29, 20, 29, 11, 4, 11, 4, 1, 4, 1, 1, 1, 1, 1, 1, 54, 54, 54, 54, 54, 54, 54, 37, 29, 29, 29, 29, 20, 20, 11, 11, 11, 11, 4, 1] 54 rigid atoms, others: [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, 36, 37, 38, 39]) total number of confs: 222 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042051 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042051 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042051/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042051 Building REAL250005042052 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042052' /scratch/stefan/7921153/working/building/REAL250005042052 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042052 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042052/0 /scratch/stefan/7921153/working/building/REAL250005042052 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 161) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/161 `/scratch/stefan/7921153/working/3D/161' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCC(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005042052.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042052.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042052/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042052 none CCCCC(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 195, 181, 65, 65, 65, 40, 21, 41, 9, 4, 9, 4, 1, 4, 1, 1, 1, 1, 1, 1, 194, 197, 197, 197, 197, 195, 195, 181, 181, 65, 41, 41, 41, 41, 22, 22, 9, 9, 9, 9, 4, 1] 201 rigid atoms, others: [42, 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, 39, 40, 41]) total number of confs: 828 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042052 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042052 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042052/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042052 Building REAL250005042053 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042053' /scratch/stefan/7921153/working/building/REAL250005042053 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042053 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042053/0 /scratch/stefan/7921153/working/building/REAL250005042053 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 162) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/162 `/scratch/stefan/7921153/working/3D/162' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005042053.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042053.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042053/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042053 none CC(C)C(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 90, 111, 90, 90, 70, 46, 70, 22, 10, 22, 10, 1, 10, 1, 1, 1, 1, 1, 1, 111, 111, 111, 111, 111, 111, 111, 90, 70, 70, 70, 70, 46, 46, 22, 22, 22, 22, 10, 1] 111 rigid atoms, others: [39, 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, 37, 38]) total number of confs: 497 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042053 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042053 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042053/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042053 Building REAL250005042054 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042054' /scratch/stefan/7921153/working/building/REAL250005042054 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042054 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042054/0 /scratch/stefan/7921153/working/building/REAL250005042054 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 163) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/163 `/scratch/stefan/7921153/working/3D/163' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)C(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005042054.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042054/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042054 none CCC(C)C(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 147, 83, 147, 83, 83, 57, 37, 57, 16, 7, 16, 7, 1, 7, 1, 1, 1, 1, 1, 1, 152, 152, 152, 152, 152, 147, 147, 147, 147, 83, 57, 57, 57, 57, 37, 37, 16, 16, 16, 16, 7, 1] 152 rigid atoms, others: [42, 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, 39, 40, 41]) total number of confs: 665 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042054 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042054 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042054/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042054 Building REAL250005042055 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042055' /scratch/stefan/7921153/working/building/REAL250005042055 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042055 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042055/0 /scratch/stefan/7921153/working/building/REAL250005042055 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 164) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/164 `/scratch/stefan/7921153/working/3D/164' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C)C(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005042055.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042055/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042055 none COC(C)C(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 39, 60, 39, 39, 25, 19, 25, 12, 5, 12, 5, 1, 5, 1, 1, 1, 1, 1, 1, 60, 60, 60, 60, 60, 60, 60, 39, 25, 25, 25, 25, 19, 19, 12, 12, 12, 12, 5, 1] 60 rigid atoms, others: [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, 36, 37, 38, 39]) total number of confs: 250 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042055 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042055 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042055/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042055 Building REAL250005042056 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042056' /scratch/stefan/7921153/working/building/REAL250005042056 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042056 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042056/0 /scratch/stefan/7921153/working/building/REAL250005042056 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 165) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/165 `/scratch/stefan/7921153/working/3D/165' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCCC(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005042056.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042056/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042056 none C=CCCC(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 174, 65, 65, 65, 42, 23, 43, 9, 4, 9, 4, 1, 4, 1, 1, 1, 1, 1, 1, 197, 197, 197, 197, 197, 174, 174, 65, 43, 43, 43, 43, 24, 24, 9, 9, 9, 9, 4, 1] 201 rigid atoms, others: [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, 36, 37, 38, 39]) total number of confs: 842 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042056 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042056 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042056/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042056 Building REAL250005042057 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042057' /scratch/stefan/7921153/working/building/REAL250005042057 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042057 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042057/0 /scratch/stefan/7921153/working/building/REAL250005042057 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 166) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/166 `/scratch/stefan/7921153/working/3D/166' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C#N)C(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005042057.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042057/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042057 none CC(C#N)C(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.1', 'N.1', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 49, 67, 67, 49, 49, 41, 30, 41, 16, 6, 16, 6, 1, 6, 1, 1, 1, 1, 1, 1, 67, 67, 67, 67, 49, 41, 41, 41, 41, 30, 30, 16, 16, 16, 16, 6, 1] 67 rigid atoms, others: [37, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 290 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042057 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042057 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042057/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042057 Building REAL250005042058 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042058' /scratch/stefan/7921153/working/building/REAL250005042058 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042058 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042058/0 /scratch/stefan/7921153/working/building/REAL250005042058 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 167) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/167 `/scratch/stefan/7921153/working/3D/167' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=C(C)C(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005042058.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042058/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042058 none CC=C(C)C(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 97 conformations in input total number of sets (complete confs): 97 using faster count positions algorithm for large data unique positions, atoms: [97, 97, 59, 97, 59, 59, 44, 28, 44, 18, 7, 18, 7, 1, 7, 1, 1, 1, 1, 1, 1, 97, 97, 97, 97, 97, 97, 97, 59, 44, 44, 44, 44, 28, 28, 18, 18, 18, 18, 7, 1] 97 rigid atoms, others: [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, 36, 37, 38, 39]) total number of confs: 365 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042058 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042058 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042058/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042058 Building REAL250005042059 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042059' /scratch/stefan/7921153/working/building/REAL250005042059 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042059 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042059/0 /scratch/stefan/7921153/working/building/REAL250005042059 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 168) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/168 `/scratch/stefan/7921153/working/3D/168' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005042059.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042059.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042059/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042059 none CCC(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [197, 146, 146, 146, 115, 66, 117, 24, 8, 24, 8, 1, 8, 1, 1, 1, 1, 1, 1, 197, 197, 197, 197, 197, 146, 117, 117, 117, 117, 70, 70, 24, 24, 24, 24, 8, 1] 201 rigid atoms, others: [36, 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, 34, 35]) total number of confs: 911 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042059 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042059 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042059/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042059 Building REAL250005042060 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042060' /scratch/stefan/7921153/working/building/REAL250005042060 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042060 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042060/0 /scratch/stefan/7921153/working/building/REAL250005042060 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 169) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/169 `/scratch/stefan/7921153/working/3D/169' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005042060.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042060.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042060/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042060 none COCCC(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 176, 66, 66, 66, 41, 24, 42, 12, 4, 12, 4, 1, 4, 1, 1, 1, 1, 1, 1, 198, 198, 198, 198, 198, 176, 176, 66, 42, 42, 42, 42, 26, 26, 12, 12, 12, 12, 4, 1] 201 rigid atoms, others: [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, 36, 37, 38, 39]) total number of confs: 833 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042060 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042060 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042060/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042060 Building REAL250005042061 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042061' /scratch/stefan/7921153/working/building/REAL250005042061 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042061 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042061/0 /scratch/stefan/7921153/working/building/REAL250005042061 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 170) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/170 `/scratch/stefan/7921153/working/3D/170' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005042061.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042061.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042061/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042061 none CC(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 24, 18, 24, 14, 6, 14, 6, 1, 6, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24, 24, 24, 24, 18, 18, 14, 14, 14, 14, 6, 1] 24 rigid atoms, others: [33, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 103 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042061 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042061 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042061/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042061 Building REAL250005042062 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042062' /scratch/stefan/7921153/working/building/REAL250005042062 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042062 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042062/0 /scratch/stefan/7921153/working/building/REAL250005042062 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 171) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/171 `/scratch/stefan/7921153/working/3D/171' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC(C)NC(=O)C1CC1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005042062.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042062/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042062 none CC(CC(C)NC(=O)C1CC1)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', '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.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [19, 9, 19, 31, 41, 41, 53, 53, 53, 77, 77, 9, 1, 9, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 31, 31, 41, 41, 41, 41, 53, 77, 77, 77, 77, 77, 9, 1] 77 rigid atoms, others: [37, 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: 283 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042062 none CC(CC(C)NC(=O)C1CC1)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', '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.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [57, 46, 28, 11, 28, 11, 1, 11, 1, 1, 1, 57, 72, 72, 72, 77, 77, 77, 77, 77, 57, 57, 57, 57, 46, 46, 28, 28, 28, 28, 11, 1, 1, 1, 1, 1, 72, 77] 77 rigid atoms, others: [32, 33, 34, 35, 6, 8, 9, 10, 31] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37]) total number of confs: 309 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042062 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042062 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042062/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042062 Building REAL250005042063 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042063' /scratch/stefan/7921153/working/building/REAL250005042063 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042063 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042063/0 /scratch/stefan/7921153/working/building/REAL250005042063 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 172) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/172 `/scratch/stefan/7921153/working/3D/172' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC(C)NC(=O)C1CCC1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005042063.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042063.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042063/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042063 none CC(CC(C)NC(=O)C1CCC1)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', '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', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [16, 8, 16, 29, 41, 41, 49, 49, 49, 89, 89, 89, 8, 1, 8, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 29, 29, 41, 41, 41, 41, 49, 89, 89, 89, 89, 89, 89, 89, 8, 1] 89 rigid atoms, others: [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, 36, 37, 38, 39]) total number of confs: 329 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042063 none CC(CC(C)NC(=O)C1CCC1)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', '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', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [67, 52, 29, 9, 29, 9, 1, 9, 1, 1, 1, 1, 67, 84, 84, 84, 89, 89, 89, 89, 89, 67, 67, 67, 67, 52, 52, 29, 29, 29, 29, 9, 1, 1, 1, 1, 1, 1, 1, 84, 89] 89 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 38] 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, 29, 30, 31, 39, 40]) total number of confs: 375 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042063 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042063 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042063/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042063 Building REAL250005042064 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042064' /scratch/stefan/7921153/working/building/REAL250005042064 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042064 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042064/0 /scratch/stefan/7921153/working/building/REAL250005042064 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 173) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/173 `/scratch/stefan/7921153/working/3D/173' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC(C)NC(=O)C1=CC(=O)[N-]O1)NC(=O)C(N)=O) `REAL250005042064.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042064.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042064/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042064 none CC(CC(C)NC(=O)C1=CC(=O)[N-]O1)NC(=O)C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 52 conformations in input total number of sets (complete confs): 52 using faster count positions algorithm for large data unique positions, atoms: [43, 31, 17, 7, 17, 7, 1, 7, 1, 1, 1, 1, 1, 1, 43, 50, 50, 50, 52, 52, 43, 43, 43, 43, 32, 32, 17, 17, 17, 17, 7, 1, 50, 52, 52] 52 rigid atoms, others: [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, 32, 33, 34]) total number of confs: 219 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042064 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042064 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042064/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042064 Building REAL250005042065 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042065' /scratch/stefan/7921153/working/building/REAL250005042065 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042065 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042065/0 /scratch/stefan/7921153/working/building/REAL250005042065 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 174) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/174 `/scratch/stefan/7921153/working/3D/174' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC(C)NC(=O)C(C)(C)C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005042065.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042065.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042065/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042065 none CC(CC(C)NC(=O)C(C)(C)C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', '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', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [17, 7, 17, 28, 37, 37, 50, 50, 50, 55, 55, 55, 7, 1, 7, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 28, 28, 37, 37, 37, 37, 50, 55, 55, 55, 55, 55, 55, 55, 55, 55, 7, 1] 55 rigid atoms, others: [42, 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, 39, 40, 41]) total number of confs: 232 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042065 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042065 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042065/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042065 Building REAL250005042066 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042066' /scratch/stefan/7921153/working/building/REAL250005042066 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042066 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042066/0 /scratch/stefan/7921153/working/building/REAL250005042066 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 175) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/175 `/scratch/stefan/7921153/working/3D/175' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC(C)NC(=O)C1(C)CC1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005042066.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042066.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042066/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042066 none CC(CC(C)NC(=O)C1(C)CC1)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', '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', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [20, 7, 20, 38, 55, 55, 81, 81, 81, 146, 146, 146, 7, 1, 7, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 39, 39, 55, 55, 55, 55, 81, 146, 146, 146, 146, 146, 146, 146, 7, 1] 146 rigid atoms, others: [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, 36, 37, 38, 39]) total number of confs: 568 number of broken/clashed sets: 13 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042066 none CC(CC(C)NC(=O)C1(C)CC1)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', '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', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [92, 58, 26, 7, 26, 7, 1, 7, 1, 1, 1, 1, 92, 133, 133, 133, 146, 146, 146, 146, 146, 92, 92, 92, 92, 58, 58, 26, 26, 26, 26, 7, 2, 2, 2, 1, 1, 1, 1, 133, 146] 146 rigid atoms, others: [35, 36, 37, 6, 8, 9, 10, 11, 38] 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, 29, 30, 31, 32, 33, 34, 39, 40]) total number of confs: 596 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042066 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042066 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042066/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042066 Building REAL250005042067 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042067' /scratch/stefan/7921153/working/building/REAL250005042067 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042067 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042067/0 /scratch/stefan/7921153/working/building/REAL250005042067 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 176) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/176 `/scratch/stefan/7921153/working/3D/176' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC(C)NC(=O)[C@@H]1C[C@H]1C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005042067.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042067/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042067 none CC(CC(C)NC(=O)[C@@H]1C[C@H]1C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 95 conformations in input total number of sets (complete confs): 95 using faster count positions algorithm for large data unique positions, atoms: [17, 6, 17, 35, 47, 47, 58, 58, 58, 95, 95, 95, 95, 95, 7, 1, 7, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 35, 35, 47, 47, 47, 47, 58, 95, 95, 95, 95, 95, 7, 1] 95 rigid atoms, others: [40, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 369 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042067 none CC(CC(C)NC(=O)[C@@H]1C[C@H]1C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 95 conformations in input total number of sets (complete confs): 95 using faster count positions algorithm for large data unique positions, atoms: [68, 57, 34, 11, 34, 11, 1, 11, 1, 1, 1, 1, 1, 1, 68, 90, 90, 90, 95, 95, 95, 95, 95, 68, 68, 68, 68, 57, 57, 34, 34, 34, 34, 11, 1, 1, 2, 2, 2, 90, 95] 95 rigid atoms, others: [34, 35, 6, 8, 9, 10, 11, 12, 13] 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, 36, 37, 38, 39, 40]) total number of confs: 399 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042067 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042067 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042067/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042067 Building REAL250005042068 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042068' /scratch/stefan/7921153/working/building/REAL250005042068 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042068 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042068/0 /scratch/stefan/7921153/working/building/REAL250005042068 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 177) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/177 `/scratch/stefan/7921153/working/3D/177' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC(C)NC(=O)[C@H]1C[C@@H]1C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005042068.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042068.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042068/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042068 none CC(CC(C)NC(=O)[C@H]1C[C@@H]1C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 10, 27, 57, 84, 82, 114, 114, 114, 199, 199, 199, 199, 199, 10, 1, 10, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 59, 59, 84, 84, 84, 84, 114, 199, 199, 199, 199, 199, 10, 1] 201 rigid atoms, others: [40, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 718 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042068 none CC(CC(C)NC(=O)[C@H]1C[C@@H]1C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [131, 86, 45, 12, 45, 12, 1, 12, 1, 1, 1, 1, 1, 1, 130, 184, 184, 184, 199, 199, 199, 199, 199, 131, 131, 131, 131, 88, 88, 45, 45, 45, 45, 12, 1, 1, 2, 2, 2, 184, 199] 201 rigid atoms, others: [34, 35, 6, 8, 9, 10, 11, 12, 13] 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, 36, 37, 38, 39, 40]) total number of confs: 806 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042068 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042068 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042068/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042068 Building REAL250005042069 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042069' /scratch/stefan/7921153/working/building/REAL250005042069 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042069 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042069/0 /scratch/stefan/7921153/working/building/REAL250005042069 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 178) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/178 `/scratch/stefan/7921153/working/3D/178' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC(C)NC(=O)C1=CC(=O)[N-]O1)NC(=O)CO) `REAL250005042069.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042069/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042069 none CC(CC(C)NC(=O)C1=CC(=O)[N-]O1)NC(=O)CO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [32, 23, 16, 6, 16, 6, 1, 6, 1, 1, 1, 1, 1, 1, 30, 41, 41, 41, 50, 32, 32, 32, 32, 26, 26, 16, 16, 16, 16, 6, 1, 41, 50, 50, 150] 159 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 30] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34]) total number of confs: 387 number of broken/clashed sets: 54 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042069 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042069 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042069/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042069 Building REAL250005042070 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042070' /scratch/stefan/7921153/working/building/REAL250005042070 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042070 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042070/0 /scratch/stefan/7921153/working/building/REAL250005042070 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 179) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/179 `/scratch/stefan/7921153/working/3D/179' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC(C)NC(=O)C1CCO1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005042070.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042070/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042070 none CC(CC(C)NC(=O)C1CCO1)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 12, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [19, 8, 19, 34, 50, 50, 55, 55, 55, 59, 59, 59, 8, 1, 8, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 35, 35, 50, 50, 50, 50, 55, 59, 59, 59, 59, 59, 8, 1] 59 rigid atoms, others: [38, 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]) total number of confs: 251 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042070 none CC(CC(C)NC(=O)C1CCO1)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 12, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [41, 29, 18, 7, 18, 7, 1, 7, 1, 1, 1, 1, 41, 55, 55, 55, 59, 59, 59, 59, 59, 41, 41, 41, 41, 29, 29, 18, 18, 18, 18, 7, 1, 1, 1, 1, 1, 55, 59] 59 rigid atoms, others: [32, 33, 34, 35, 36, 6, 8, 9, 10, 11] 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, 29, 30, 31, 37, 38]) total number of confs: 237 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042070 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042070 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042070/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042070 Building REAL250005042071 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042071' /scratch/stefan/7921153/working/building/REAL250005042071 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042071 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042071/0 /scratch/stefan/7921153/working/building/REAL250005042071 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 180) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/180 `/scratch/stefan/7921153/working/3D/180' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC(C)NC(=O)C1COC1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005042071.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042071.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042071/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042071 none CC(CC(C)NC(=O)C1COC1)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 165 conformations in input total number of sets (complete confs): 165 using faster count positions algorithm for large data unique positions, atoms: [25, 10, 25, 51, 73, 73, 103, 103, 103, 165, 165, 165, 10, 1, 10, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 52, 52, 73, 73, 73, 73, 103, 165, 165, 165, 165, 165, 10, 1] 165 rigid atoms, others: [38, 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]) total number of confs: 626 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042071 none CC(CC(C)NC(=O)C1COC1)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 165 conformations in input total number of sets (complete confs): 165 using faster count positions algorithm for large data unique positions, atoms: [110, 74, 37, 11, 37, 11, 1, 11, 1, 1, 1, 1, 110, 153, 153, 153, 165, 165, 165, 165, 165, 110, 110, 110, 110, 76, 76, 37, 37, 37, 37, 11, 1, 1, 1, 1, 1, 153, 165] 165 rigid atoms, others: [32, 33, 34, 35, 36, 6, 8, 9, 10, 11] 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, 29, 30, 31, 37, 38]) total number of confs: 670 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042071 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042071 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042071/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042071 Building REAL250005042072 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042072' /scratch/stefan/7921153/working/building/REAL250005042072 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042072 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042072/0 /scratch/stefan/7921153/working/building/REAL250005042072 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 181) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/181 `/scratch/stefan/7921153/working/3D/181' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC(C)NC(=O)C1=CC(=O)[N-]O1)NC(=O)C=CCO) `REAL250005042072.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042072.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042072/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042072 none CC(CC(C)NC(=O)C1=CC(=O)[N-]O1)NC(=O)C=CCO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [63, 34, 14, 4, 14, 4, 1, 4, 1, 1, 1, 1, 1, 1, 62, 97, 97, 97, 183, 183, 198, 63, 63, 63, 63, 35, 35, 14, 14, 14, 14, 4, 1, 97, 183, 183, 198, 198, 594] 603 rigid atoms, others: [32, 6, 8, 9, 10, 11, 12, 13] 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, 33, 34, 35, 36, 37, 38]) total number of confs: 1344 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042072 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042072 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042072/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042072 Building REAL250005042073 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042073' /scratch/stefan/7921153/working/building/REAL250005042073 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042073 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042073/0 /scratch/stefan/7921153/working/building/REAL250005042073 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 182) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/182 `/scratch/stefan/7921153/working/3D/182' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC=CC(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005042073.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042073.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042073/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042073 none CCC=CC(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 156, 156, 100, 100, 100, 67, 36, 68, 13, 4, 13, 4, 1, 4, 1, 1, 1, 1, 1, 1, 198, 198, 198, 198, 198, 156, 156, 100, 68, 68, 68, 68, 37, 37, 13, 13, 13, 13, 4, 1] 201 rigid atoms, others: [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, 36, 37, 38, 39]) total number of confs: 854 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042073 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042073 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042073/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042073 Building REAL250005042074 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042074' /scratch/stefan/7921153/working/building/REAL250005042074 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042074 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042074/0 /scratch/stefan/7921153/working/building/REAL250005042074 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 183) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/183 `/scratch/stefan/7921153/working/3D/183' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCC(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005042074.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042074/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042074 none C#CCCC(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [198, 198, 182, 83, 83, 83, 59, 35, 60, 14, 4, 14, 4, 1, 4, 1, 1, 1, 1, 1, 1, 198, 198, 198, 182, 182, 83, 60, 60, 60, 60, 36, 36, 14, 14, 14, 14, 4, 1] 201 rigid atoms, others: [38, 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]) total number of confs: 857 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042074 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042074 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042074/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042074 Building REAL250005042075 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042075' /scratch/stefan/7921153/working/building/REAL250005042075 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042075 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042075/0 /scratch/stefan/7921153/working/building/REAL250005042075 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 184) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/184 `/scratch/stefan/7921153/working/3D/184' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(O)C(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005042075.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042075.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042075/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042075 none C=CC(O)C(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [37, 36, 24, 36, 24, 24, 18, 13, 19, 9, 3, 9, 3, 1, 3, 1, 1, 1, 1, 1, 1, 37, 37, 37, 36, 108, 24, 19, 19, 19, 19, 15, 15, 9, 9, 9, 9, 3, 1] 111 rigid atoms, others: [38, 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]) total number of confs: 287 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042075 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042075 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042075/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042075 Building REAL250005042076 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042076' /scratch/stefan/7921153/working/building/REAL250005042076 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042076 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042076/0 /scratch/stefan/7921153/working/building/REAL250005042076 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 185) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/185 `/scratch/stefan/7921153/working/3D/185' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)C(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005042076.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042076/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042076 none CC(O)C(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [47, 33, 47, 33, 33, 26, 19, 26, 11, 4, 11, 4, 1, 4, 1, 1, 1, 1, 1, 1, 47, 47, 47, 47, 141, 33, 26, 26, 26, 26, 19, 19, 11, 11, 11, 11, 4, 1] 141 rigid atoms, others: [37, 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: 358 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042076 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042076 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042076/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042076 Building REAL250005042077 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042077' /scratch/stefan/7921153/working/building/REAL250005042077 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042077 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042077/0 /scratch/stefan/7921153/working/building/REAL250005042077 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 186) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/186 `/scratch/stefan/7921153/working/3D/186' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)C(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005042077.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042077.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042077/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042077 none CC(=O)C(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [65, 60, 65, 60, 60, 47, 36, 47, 20, 8, 20, 8, 1, 8, 1, 1, 1, 1, 1, 1, 65, 65, 65, 60, 47, 47, 47, 47, 37, 37, 20, 20, 20, 20, 8, 1] 65 rigid atoms, others: [35, 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]) total number of confs: 261 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042077 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042077 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042077/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042077 Building REAL250005042078 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042078' /scratch/stefan/7921153/working/building/REAL250005042078 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042078 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042078/0 /scratch/stefan/7921153/working/building/REAL250005042078 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 187) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/187 `/scratch/stefan/7921153/working/3D/187' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC(C)NC(=O)C1(F)CC1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005042078.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042078.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042078/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042078 none CC(CC(C)NC(=O)C1(F)CC1)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 15, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [24, 9, 24, 46, 70, 69, 104, 104, 104, 153, 153, 153, 9, 1, 9, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 47, 47, 70, 70, 70, 70, 104, 153, 153, 153, 153, 9, 1] 154 rigid atoms, others: [37, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 577 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042078 none CC(CC(C)NC(=O)C1(F)CC1)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 15, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [104, 68, 34, 11, 34, 11, 1, 11, 1, 1, 1, 1, 103, 145, 145, 145, 153, 153, 153, 153, 153, 104, 104, 104, 104, 71, 71, 34, 34, 34, 34, 11, 1, 1, 1, 1, 145, 153] 154 rigid atoms, others: [32, 33, 34, 35, 6, 8, 9, 10, 11] 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, 29, 30, 31, 36, 37]) total number of confs: 626 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042078 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042078 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042078/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042078 Building REAL250005042079 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042079' /scratch/stefan/7921153/working/building/REAL250005042079 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042079 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042079/0 /scratch/stefan/7921153/working/building/REAL250005042079 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 188) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/188 `/scratch/stefan/7921153/working/3D/188' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=C(F)C(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005042079.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042079/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042079 none CC=C(F)C(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 15, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [118, 118, 77, 118, 77, 77, 57, 31, 58, 12, 4, 12, 4, 1, 4, 1, 1, 1, 1, 1, 1, 118, 118, 118, 118, 77, 58, 58, 58, 58, 33, 33, 12, 12, 12, 12, 4, 1] 119 rigid atoms, others: [37, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 467 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042079 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042079 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042079/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042079 Building REAL250005042080 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042080' /scratch/stefan/7921153/working/building/REAL250005042080 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042080 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042080/0 /scratch/stefan/7921153/working/building/REAL250005042080 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 189) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/189 `/scratch/stefan/7921153/working/3D/189' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC(C)NC(=O)C(C)CO)NC(=O)C1=CC(=O)[N-]O1) `REAL250005042080.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042080/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042080 none CC(CC(C)NC(=O)C(C)CO)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 12, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [6, 4, 6, 8, 10, 10, 14, 14, 14, 20, 20, 20, 4, 1, 4, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 8, 8, 10, 10, 10, 10, 14, 20, 20, 20, 20, 20, 20, 60, 4, 1] 60 rigid atoms, others: [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, 36, 37, 38, 39]) total number of confs: 146 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042080 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042080 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042080/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042080 Building REAL250005042081 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042081' /scratch/stefan/7921153/working/building/REAL250005042081 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042081 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042081/0 /scratch/stefan/7921153/working/building/REAL250005042081 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 190) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/190 `/scratch/stefan/7921153/working/3D/190' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC(C)NC(=O)C1(O)CC1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005042081.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042081.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042081/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042081 none CC(CC(C)NC(=O)C1(O)CC1)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 228 conformations in input total number of sets (complete confs): 228 using faster count positions algorithm for large data unique positions, atoms: [20, 7, 20, 36, 49, 49, 64, 64, 64, 76, 76, 76, 7, 1, 7, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 36, 36, 49, 49, 49, 49, 64, 228, 76, 76, 76, 76, 7, 1] 228 rigid atoms, others: [38, 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]) total number of confs: 542 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042081 none CC(CC(C)NC(=O)C1(O)CC1)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 228 conformations in input total number of sets (complete confs): 228 using faster count positions algorithm for large data unique positions, atoms: [58, 45, 27, 11, 27, 11, 1, 11, 1, 1, 1, 1, 58, 72, 72, 72, 76, 76, 76, 76, 76, 58, 58, 58, 58, 45, 45, 27, 27, 27, 27, 11, 6, 1, 1, 1, 1, 72, 76] 228 rigid atoms, others: [33, 34, 35, 36, 6, 8, 9, 10, 11] 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, 29, 30, 31, 32, 37, 38]) total number of confs: 318 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042081 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042081 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042081/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042081 Building REAL250005042082 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042082' /scratch/stefan/7921153/working/building/REAL250005042082 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042082 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042082/0 /scratch/stefan/7921153/working/building/REAL250005042082 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 191) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/191 `/scratch/stefan/7921153/working/3D/191' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC(C)NC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CCC1) `REAL250005042082.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042082/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042082 none CC(CC(C)NC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 5, 5, 7, 7, 7, 7, 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, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [13, 7, 13, 21, 29, 29, 37, 37, 37, 38, 38, 38, 38, 38, 7, 1, 7, 1, 1, 1, 1, 13, 13, 13, 13, 22, 22, 29, 29, 29, 29, 37, 38, 7, 1, 1, 1, 1, 1] 38 rigid atoms, others: [34, 35, 36, 37, 38, 15, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 148 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042082 none CC(CC(C)NC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 5, 5, 7, 7, 7, 7, 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, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [33, 23, 12, 5, 12, 5, 1, 5, 1, 1, 1, 1, 1, 1, 33, 38, 38, 38, 38, 38, 38, 33, 33, 33, 33, 23, 23, 12, 12, 12, 12, 5, 1, 38, 38, 38, 38, 38, 38] 38 rigid atoms, others: [32, 6, 8, 9, 10, 11, 12, 13] 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, 33, 34, 35, 36, 37, 38]) total number of confs: 163 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042082 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042082 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042082/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042082 Building REAL250005042083 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042083' /scratch/stefan/7921153/working/building/REAL250005042083 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042083 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042083/0 /scratch/stefan/7921153/working/building/REAL250005042083 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 192) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/192 `/scratch/stefan/7921153/working/3D/192' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=CC(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005042083.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042083/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042083 none CC=CC(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 124 conformations in input total number of sets (complete confs): 124 using faster count positions algorithm for large data unique positions, atoms: [122, 122, 96, 96, 96, 70, 42, 72, 19, 7, 19, 7, 1, 7, 1, 1, 1, 1, 1, 1, 122, 122, 122, 122, 122, 96, 72, 72, 72, 72, 44, 44, 19, 19, 19, 19, 7, 1] 124 rigid atoms, others: [37, 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: 516 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042083 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042083 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042083/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042083 Building REAL250005042084 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042084' /scratch/stefan/7921153/working/building/REAL250005042084 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042084 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042084/0 /scratch/stefan/7921153/working/building/REAL250005042084 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 193) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/193 `/scratch/stefan/7921153/working/3D/193' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC(C)NC(=O)C1=CC(=O)[N-]O1)NC(=O)C=CCF) `REAL250005042084.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042084.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042084/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042084 none CC(CC(C)NC(=O)C1=CC(=O)[N-]O1)NC(=O)C=CCF NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 5, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 156 conformations in input total number of sets (complete confs): 156 using faster count positions algorithm for large data unique positions, atoms: [50, 27, 13, 4, 13, 4, 1, 4, 1, 1, 1, 1, 1, 1, 49, 77, 77, 77, 143, 143, 153, 50, 50, 50, 50, 28, 28, 13, 13, 13, 13, 4, 1, 77, 143, 143, 153, 153] 156 rigid atoms, others: [32, 6, 8, 9, 10, 11, 12, 13] 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, 33, 34, 35, 36, 37]) total number of confs: 583 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042084 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042084 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042084/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042084 Building REAL250005042085 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042085' /scratch/stefan/7921153/working/building/REAL250005042085 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types Protomer extracton resulted in 0 protomers Marking REAL250005042085 as failed and skipping /scratch/stefan/7921153/working /scratch/stefan/7921153 `/scratch/stefan/7921153/working/building/REAL250005042085' -> `/scratch/stefan/7921153/failed/REAL250005042085' Building REAL250005042086 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042086' /scratch/stefan/7921153/working/building/REAL250005042086 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042086 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042086/0 /scratch/stefan/7921153/working/building/REAL250005042086 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 194) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/194 `/scratch/stefan/7921153/working/3D/194' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC(C)NC(=O)[C@H](C)O)NC(=O)C1=CC(=O)[N-]O1) `REAL250005042086.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042086.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042086/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042086 none CC(CC(C)NC(=O)[C@H](C)O)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 12, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [21, 8, 21, 34, 43, 43, 54, 54, 54, 58, 58, 58, 8, 1, 8, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 34, 34, 43, 43, 43, 43, 54, 58, 58, 58, 174, 8, 1] 174 rigid atoms, others: [37, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 415 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042086 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042086 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042086/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042086 Building REAL250005042087 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042087' /scratch/stefan/7921153/working/building/REAL250005042087 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042087 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042087/0 /scratch/stefan/7921153/working/building/REAL250005042087 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 195) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/195 `/scratch/stefan/7921153/working/3D/195' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CON=CC(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005042087.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042087/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042087 none CON=CC(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [47, 47, 47, 27, 27, 27, 20, 15, 22, 10, 4, 10, 4, 1, 4, 1, 1, 1, 1, 1, 1, 47, 47, 47, 47, 27, 22, 22, 22, 22, 18, 18, 10, 10, 10, 10, 4, 1] 48 rigid atoms, others: [37, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 189 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042087 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042087 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042087/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042087 Building REAL250005042088 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042088' /scratch/stefan/7921153/working/building/REAL250005042088 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042088 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042088/0 /scratch/stefan/7921153/working/building/REAL250005042088 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 196) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/196 `/scratch/stefan/7921153/working/3D/196' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC(C)NC(=O)[C@@H]1C[C@H]1C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005042088.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042088.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042088/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042088 none CC(CC(C)NC(=O)[C@@H]1C[C@H]1C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 95 conformations in input total number of sets (complete confs): 95 using faster count positions algorithm for large data unique positions, atoms: [17, 6, 17, 35, 47, 47, 58, 58, 58, 95, 95, 95, 95, 95, 7, 1, 7, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 35, 35, 47, 47, 47, 47, 58, 95, 95, 95, 95, 95, 7, 1] 95 rigid atoms, others: [40, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 369 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042088 none CC(CC(C)NC(=O)[C@@H]1C[C@H]1C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 95 conformations in input total number of sets (complete confs): 95 using faster count positions algorithm for large data unique positions, atoms: [68, 57, 34, 11, 34, 11, 1, 11, 1, 1, 1, 1, 1, 1, 68, 90, 90, 90, 95, 95, 95, 95, 95, 68, 68, 68, 68, 57, 57, 34, 34, 34, 34, 11, 1, 1, 2, 2, 2, 90, 95] 95 rigid atoms, others: [34, 35, 6, 8, 9, 10, 11, 12, 13] 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, 36, 37, 38, 39, 40]) total number of confs: 399 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042088 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042088 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042088/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042088 Building REAL250005042089 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042089' /scratch/stefan/7921153/working/building/REAL250005042089 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042089 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042089/0 /scratch/stefan/7921153/working/building/REAL250005042089 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 197) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/197 `/scratch/stefan/7921153/working/3D/197' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC(C)NC(=O)C(C)(C)O)NC(=O)C1=CC(=O)[N-]O1) `REAL250005042089.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042089.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042089/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042089 none CC(CC(C)NC(=O)C(C)(C)O)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 12, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 240 conformations in input total number of sets (complete confs): 240 using faster count positions algorithm for large data unique positions, atoms: [24, 10, 24, 37, 49, 49, 61, 61, 61, 80, 80, 80, 10, 1, 10, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 37, 37, 49, 49, 49, 49, 61, 80, 80, 80, 80, 80, 80, 240, 10, 1] 240 rigid atoms, others: [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, 36, 37, 38, 39]) total number of confs: 599 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042089 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042089 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042089/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042089 Building REAL250005042090 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042090' /scratch/stefan/7921153/working/building/REAL250005042090 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042090 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042090/0 /scratch/stefan/7921153/working/building/REAL250005042090 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 198) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/198 `/scratch/stefan/7921153/working/3D/198' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C(C)CC(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005042090.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042090.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042090/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042090 none C=C(C)CC(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 99, 99, 99, 66, 40, 67, 15, 4, 15, 4, 1, 4, 1, 1, 1, 1, 1, 1, 199, 199, 199, 199, 199, 199, 199, 99, 67, 67, 67, 67, 42, 42, 15, 15, 15, 15, 4, 1] 201 rigid atoms, others: [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, 36, 37, 38, 39]) total number of confs: 832 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042090 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042090 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042090/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042090 Building REAL250005042091 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042091' /scratch/stefan/7921153/working/building/REAL250005042091 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042091 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042091/0 /scratch/stefan/7921153/working/building/REAL250005042091 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 199) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/199 `/scratch/stefan/7921153/working/3D/199' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005042091.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042091.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042091/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042091 none C=CCC(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [200, 200, 102, 102, 102, 74, 45, 76, 15, 4, 15, 4, 1, 4, 1, 1, 1, 1, 1, 1, 200, 200, 200, 200, 200, 102, 76, 76, 76, 76, 49, 49, 15, 15, 15, 15, 4, 1] 201 rigid atoms, others: [37, 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: 880 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042091 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042091 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042091/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042091 Building REAL250005042092 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042092' /scratch/stefan/7921153/working/building/REAL250005042092 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005042092 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042092/0 /scratch/stefan/7921153/working/building/REAL250005042092 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 200) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/200 `/scratch/stefan/7921153/working/3D/200' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC(C)NC(=O)C1=CC(=O)[N-]O1)NC(=O)C[NH+](C)C) `REAL250005042092.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042092.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042092/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042092 none CC(CC(C)NC(=O)C1=CC(=O)[N-]O1)NC(=O)C[NH+](C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 3, 2, 3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 3, 3, 3, 3, 2, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4] 5 rigid atoms, others: [33, 6, 8, 9, 10, 11, 12, 13] 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, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 26 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042092 /scratch/stefan/7921153/working /scratch/stefan/7921153 mkdir: created directory `1' /scratch/stefan/7921153/working/building/REAL250005042092/1 /scratch/stefan/7921153/working/building/REAL250005042092 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 1 (index: 201) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/201 `/scratch/stefan/7921153/working/3D/201' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC(C)NC(=O)C1=CC(=O)[N-]O1)NC(=O)CN(C)C) `REAL250005042092.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005042092.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042092/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.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: REAL250005042092 none CC(CC(C)NC(=O)C1=CC(=O)[N-]O1)NC(=O)CN(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 132 conformations in input total number of sets (complete confs): 132 using faster count positions algorithm for large data unique positions, atoms: [45, 27, 15, 5, 15, 5, 1, 5, 1, 1, 1, 1, 1, 1, 41, 63, 63, 63, 125, 129, 129, 45, 45, 45, 45, 32, 32, 15, 15, 15, 15, 5, 1, 63, 125, 125, 129, 129, 129, 129, 129, 129] 132 rigid atoms, others: [32, 6, 8, 9, 10, 11, 12, 13] 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, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 576 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042092 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042092 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 1: /scratch/stefan/7921153/working/building/REAL250005042092/1.* 0: /scratch/stefan/7921153/working/building/REAL250005042092/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042092 Building REAL250005042093 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042093' /scratch/stefan/7921153/working/building/REAL250005042093 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042093 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042093/0 /scratch/stefan/7921153/working/building/REAL250005042093 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 202) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/202 `/scratch/stefan/7921153/working/3D/202' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC(C)NC(=O)C1=CC(=O)[N-]O1)NC(=O)CC#N) `REAL250005042093.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042093.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042093/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042093 none CC(CC(C)NC(=O)C1=CC(=O)[N-]O1)NC(=O)CC#N NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.1', 'N.1', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 122 conformations in input total number of sets (complete confs): 122 using faster count positions algorithm for large data unique positions, atoms: [53, 37, 18, 6, 18, 6, 1, 6, 1, 1, 1, 1, 1, 1, 51, 71, 72, 71, 119, 119, 53, 53, 53, 53, 40, 40, 18, 18, 18, 18, 6, 1, 72, 119, 119] 122 rigid atoms, others: [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, 32, 33, 34]) total number of confs: 526 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042093 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042093 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042093/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042093 Building REAL250005042094 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042094' /scratch/stefan/7921153/working/building/REAL250005042094 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042094 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042094/0 /scratch/stefan/7921153/working/building/REAL250005042094 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 203) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/203 `/scratch/stefan/7921153/working/3D/203' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC(C)NC(=O)C1CC1F)NC(=O)C1=CC(=O)[N-]O1) `REAL250005042094.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042094/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042094 none CC(CC(C)NC(=O)C1CC1F)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 15, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [27, 10, 27, 59, 83, 83, 109, 109, 109, 176, 176, 176, 10, 1, 10, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 60, 60, 83, 83, 83, 83, 109, 176, 176, 176, 176, 10, 1] 176 rigid atoms, others: [37, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 660 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042094 none CC(CC(C)NC(=O)C1CC1F)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 15, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [121, 80, 39, 13, 39, 13, 1, 13, 1, 1, 1, 1, 121, 162, 162, 162, 176, 176, 176, 176, 176, 121, 121, 121, 121, 83, 83, 39, 39, 39, 39, 13, 1, 1, 1, 1, 162, 176] 176 rigid atoms, others: [32, 33, 34, 35, 6, 8, 9, 10, 11] 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, 29, 30, 31, 36, 37]) total number of confs: 732 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042094 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042094 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042094/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042094 Building REAL250005042095 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042095' /scratch/stefan/7921153/working/building/REAL250005042095 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042095 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042095/0 /scratch/stefan/7921153/working/building/REAL250005042095 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 204) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/204 `/scratch/stefan/7921153/working/3D/204' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC(C)NC(=O)C1=CC(=O)[N-]O1)NC(=O)CCF) `REAL250005042095.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042095/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042095 none CC(CC(C)NC(=O)C1=CC(=O)[N-]O1)NC(=O)CCF NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [66, 34, 14, 4, 14, 4, 1, 4, 1, 1, 1, 1, 1, 1, 65, 98, 98, 98, 198, 198, 66, 66, 66, 66, 37, 37, 14, 14, 14, 14, 4, 1, 98, 198, 198, 198, 198] 201 rigid atoms, others: [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, 32, 33, 34, 35, 36]) total number of confs: 813 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042095 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042095 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042095/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042095 Building REAL250005042096 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042096' /scratch/stefan/7921153/working/building/REAL250005042096 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042096 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042096/0 /scratch/stefan/7921153/working/building/REAL250005042096 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 205) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/205 `/scratch/stefan/7921153/working/3D/205' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H](C)C(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005042096.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042096/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042096 none CO[C@H](C)C(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [67, 66, 40, 66, 66, 40, 40, 32, 22, 33, 12, 4, 12, 4, 1, 4, 1, 1, 1, 1, 1, 1, 67, 67, 67, 66, 66, 66, 40, 33, 33, 33, 33, 24, 24, 12, 12, 12, 12, 4, 1] 68 rigid atoms, others: [40, 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]) total number of confs: 300 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042096 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042096 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042096/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042096 Building REAL250005042097 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042097' /scratch/stefan/7921153/working/building/REAL250005042097 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042097 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042097/0 /scratch/stefan/7921153/working/building/REAL250005042097 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 206) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/206 `/scratch/stefan/7921153/working/3D/206' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC(C)NC(=O)[C@@H](C)O)NC(=O)C1=CC(=O)[N-]O1) `REAL250005042097.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042097/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042097 none CC(CC(C)NC(=O)[C@@H](C)O)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 12, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 282 conformations in input total number of sets (complete confs): 282 using faster count positions algorithm for large data unique positions, atoms: [22, 10, 22, 41, 61, 60, 79, 79, 79, 94, 94, 94, 10, 1, 10, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 42, 42, 61, 61, 61, 61, 79, 94, 94, 94, 282, 10, 1] 282 rigid atoms, others: [37, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 689 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042097 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042097 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042097/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042097 Building REAL250005042098 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042098' /scratch/stefan/7921153/working/building/REAL250005042098 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042098 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042098/0 /scratch/stefan/7921153/working/building/REAL250005042098 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 207) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/207 `/scratch/stefan/7921153/working/3D/207' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C1CC1C(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005042098.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042098.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042098/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042098 none C=C1CC1C(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 82, 82, 82, 66, 42, 66, 19, 6, 19, 6, 1, 6, 1, 1, 1, 1, 1, 1, 142, 142, 142, 142, 142, 82, 66, 66, 66, 66, 42, 42, 19, 19, 19, 19, 6, 1] 142 rigid atoms, others: [38, 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]) total number of confs: 528 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042098 none C=C1CC1C(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 142 conformations in input total number of sets (complete confs): 142 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 13, 13, 13, 51, 51, 86, 119, 119, 139, 139, 139, 142, 142, 142, 142, 142, 1, 1, 1, 1, 1, 13, 51, 51, 51, 51, 89, 89, 119, 119, 119, 119, 139, 142] 142 rigid atoms, others: [0, 1, 2, 3, 4, 21, 22, 23, 24, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 606 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042098 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042098 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042098/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042098 Building REAL250005042099 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042099' /scratch/stefan/7921153/working/building/REAL250005042099 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042099 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042099/0 /scratch/stefan/7921153/working/building/REAL250005042099 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 208) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/208 `/scratch/stefan/7921153/working/3D/208' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC1C(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005042099.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042099.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042099/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042099 none CC1=CC1C(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 156 conformations in input total number of sets (complete confs): 156 using faster count positions algorithm for large data unique positions, atoms: [156, 156, 156, 90, 90, 90, 67, 45, 67, 21, 8, 21, 8, 1, 8, 1, 1, 1, 1, 1, 1, 156, 156, 156, 156, 156, 90, 67, 67, 67, 67, 45, 45, 21, 21, 21, 21, 8, 1] 156 rigid atoms, others: [38, 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]) total number of confs: 559 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042099 none CC1=CC1C(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 156 conformations in input total number of sets (complete confs): 156 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 13, 13, 13, 51, 51, 90, 127, 127, 151, 151, 151, 156, 156, 156, 156, 156, 2, 2, 2, 1, 1, 13, 51, 51, 51, 51, 93, 93, 127, 127, 127, 127, 151, 156] 156 rigid atoms, others: [0, 1, 2, 3, 4, 24, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 692 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042099 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042099 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042099/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042099 Building REAL250005042100 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042100' /scratch/stefan/7921153/working/building/REAL250005042100 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042100 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042100/0 /scratch/stefan/7921153/working/building/REAL250005042100 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 209) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/209 `/scratch/stefan/7921153/working/3D/209' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005042100.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042100.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042100/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042100 none C=CC(=O)NC(C)CC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 109 conformations in input total number of sets (complete confs): 109 using faster count positions algorithm for large data unique positions, atoms: [108, 108, 108, 108, 76, 45, 77, 22, 7, 22, 7, 1, 7, 1, 1, 1, 1, 1, 1, 108, 108, 108, 108, 77, 77, 77, 77, 46, 46, 22, 22, 22, 22, 7, 1] 109 rigid atoms, others: [34, 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: 449 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042100 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042100 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042100/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042100 Building REAL250005042101 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042101' /scratch/stefan/7921153/working/building/REAL250005042101 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042101 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042101/0 /scratch/stefan/7921153/working/building/REAL250005042101 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 210) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/210 `/scratch/stefan/7921153/working/3D/210' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N1CC2(C1)CCN(C(=O)C1=CC(=O)[N-]O1)C2) `REAL250005042101.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042101.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042101/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042101 none CCC(=O)N1CC2(C1)CCN(C(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 36, 20, 36, 20, 20, 20, 20, 20, 20, 9, 1, 9, 1, 1, 1, 1, 1, 1, 20, 46, 46, 46, 46, 46, 20, 20, 20, 20, 20, 20, 20, 20, 1, 20, 20] 46 rigid atoms, others: [33, 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, 34, 35]) total number of confs: 155 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042101 none CCC(=O)N1CC2(C1)CCN(C(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [11, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 20, 20, 20, 20, 20, 1, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 20, 1, 1] 46 rigid atoms, others: [32, 2, 35, 4, 5, 6, 7, 8, 9, 10, 11, 34, 19, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 3, 33, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042101 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042101 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042101/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042101 Building REAL250005042102 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042102' /scratch/stefan/7921153/working/building/REAL250005042102 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042102 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042102/0 /scratch/stefan/7921153/working/building/REAL250005042102 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 211) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/211 `/scratch/stefan/7921153/working/3D/211' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CC2(C1)CCN(C(=O)C1=CC(=O)[N-]O1)C2) `REAL250005042102.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042102/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042102 none CC(=O)N1CC2(C1)CCN(C(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [23, 14, 23, 14, 14, 14, 14, 14, 14, 9, 1, 9, 1, 1, 1, 1, 1, 1, 14, 23, 23, 23, 14, 14, 14, 14, 14, 14, 14, 14, 1, 14, 14] 23 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32]) total number of confs: 65 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042102 none CC(=O)N1CC2(C1)CCN(C(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 14, 14, 14, 14, 14, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 14, 1, 1] 23 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 9, 10, 18, 22, 23, 24, 25, 26, 27, 28, 29, 31] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 30]) total number of confs: 40 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042102 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042102 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042102/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042102 Building REAL250005042103 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042103' /scratch/stefan/7921153/working/building/REAL250005042103 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042103 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042103/0 /scratch/stefan/7921153/working/building/REAL250005042103 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 212) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/212 `/scratch/stefan/7921153/working/3D/212' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(C1=CC(=O)[N-]O1)N1CCC2(CN(C(=O)C3CC3)C2)C1) `REAL250005042103.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042103.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042103/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042103 none O=C(C1=CC(=O)[N-]O1)N1CCC2(CN(C(=O)C3CC3)C2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [36, 15, 36, 50, 50, 50, 50, 50, 15, 15, 15, 15, 15, 8, 1, 8, 1, 1, 1, 15, 15, 50, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 1, 15, 15, 15, 15] 50 rigid atoms, others: [32, 14, 16, 17, 18, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 33, 34, 35, 36]) total number of confs: 117 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: REAL250005042103 none O=C(C1=CC(=O)[N-]O1)N1CCC2(CN(C(=O)C3CC3)C2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [7, 1, 7, 25, 25, 25, 25, 25, 1, 1, 1, 1, 1, 1, 1, 4, 4, 15, 15, 1, 1, 25, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 1, 1, 1, 1] 50 rigid atoms, others: [1, 34, 35, 36, 33, 8, 9, 10, 11, 12, 13, 14, 19, 20, 22, 23, 24, 25, 26, 27] set([0, 32, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 21, 28, 29, 30, 31]) total number of confs: 73 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042103 none O=C(C1=CC(=O)[N-]O1)N1CCC2(CN(C(=O)C3CC3)C2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [8, 1, 1, 1, 1, 1, 1, 1, 8, 25, 25, 25, 25, 25, 25, 37, 37, 50, 50, 25, 25, 1, 25, 25, 25, 25, 25, 25, 50, 50, 50, 50, 50, 25, 25, 25, 25] 50 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 21] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042103 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042103 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042103/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042103 Building REAL250005042104 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042104' /scratch/stefan/7921153/working/building/REAL250005042104 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042104 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042104/0 /scratch/stefan/7921153/working/building/REAL250005042104 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 213) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/213 `/scratch/stefan/7921153/working/3D/213' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)N1CC2(C1)CCN(C(=O)C1=CC(=O)[N-]O1)C2) `REAL250005042104.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042104.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042104/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042104 none COCC(=O)N1CC2(C1)CCN(C(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [90, 86, 43, 25, 43, 25, 25, 25, 25, 25, 25, 9, 1, 9, 1, 1, 1, 1, 1, 1, 25, 90, 90, 90, 86, 86, 25, 25, 25, 25, 25, 25, 25, 25, 1, 25, 25] 90 rigid atoms, others: [34, 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, 35, 36]) total number of confs: 300 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042104 none COCC(=O)N1CC2(C1)CCN(C(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [48, 25, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 25, 25, 25, 25, 25, 1, 48, 48, 48, 26, 26, 1, 1, 1, 1, 1, 1, 1, 1, 25, 1, 1] 90 rigid atoms, others: [32, 33, 3, 36, 5, 6, 7, 8, 9, 10, 11, 12, 35, 20, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 34, 4, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042104 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042104 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042104/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042104 Building REAL250005042105 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042105' /scratch/stefan/7921153/working/building/REAL250005042105 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042105 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042105/0 /scratch/stefan/7921153/working/building/REAL250005042105 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 214) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/214 `/scratch/stefan/7921153/working/3D/214' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(=O)N1CC2(C1)CCN(C(=O)C1=CC(=O)[N-]O1)C2) `REAL250005042105.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042105/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042105 none CCCC(=O)N1CC2(C1)CCN(C(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 87, 47, 28, 47, 28, 28, 28, 28, 28, 28, 8, 1, 8, 1, 1, 1, 1, 1, 1, 28, 89, 89, 89, 89, 89, 87, 87, 28, 28, 28, 28, 28, 28, 28, 28, 1, 28, 28] 89 rigid atoms, others: [36, 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, 37, 38]) total number of confs: 315 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042105 none CCCC(=O)N1CC2(C1)CCN(C(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [34, 23, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 28, 28, 28, 28, 28, 1, 40, 40, 40, 39, 39, 24, 24, 1, 1, 1, 1, 1, 1, 1, 1, 28, 1, 1] 89 rigid atoms, others: [32, 33, 34, 3, 5, 6, 7, 8, 9, 10, 11, 12, 37, 35, 20, 38, 28, 29, 30, 31] set([0, 1, 2, 4, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 36]) total number of confs: 242 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042105 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042105 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042105/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042105 Building REAL250005042106 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042106' /scratch/stefan/7921153/working/building/REAL250005042106 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042106 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042106/0 /scratch/stefan/7921153/working/building/REAL250005042106 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 215) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/215 `/scratch/stefan/7921153/working/3D/215' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N1CC2(C1)CCN(C(=O)C1=CC(=O)[N-]O1)C2) `REAL250005042106.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042106/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042106 none CC(C)C(=O)N1CC2(C1)CCN(C(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [49, 42, 49, 20, 42, 20, 20, 20, 20, 20, 20, 10, 1, 10, 1, 1, 1, 1, 1, 1, 20, 49, 49, 49, 49, 49, 49, 49, 20, 20, 20, 20, 20, 20, 20, 20, 1, 20, 20] 49 rigid atoms, others: [36, 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, 37, 38]) total number of confs: 150 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042106 none CC(C)C(=O)N1CC2(C1)CCN(C(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [15, 5, 15, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 20, 20, 20, 20, 20, 1, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 20, 1, 1] 49 rigid atoms, others: [32, 33, 34, 3, 5, 6, 7, 8, 9, 10, 11, 12, 37, 35, 20, 38, 28, 29, 30, 31] set([0, 1, 2, 4, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 36]) total number of confs: 84 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042106 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042106 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042106/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042106 Building REAL250005042107 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042107' /scratch/stefan/7921153/working/building/REAL250005042107 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042107 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042107/0 /scratch/stefan/7921153/working/building/REAL250005042107 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 216) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/216 `/scratch/stefan/7921153/working/3D/216' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C(=O)N1CC2(C1)CCN(C(=O)C1=CC(=O)[N-]O1)C2) `REAL250005042107.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042107/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042107 none NC(=O)C(=O)N1CC2(C1)CCN(C(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [47, 35, 47, 21, 35, 21, 21, 21, 21, 21, 21, 10, 1, 10, 1, 1, 1, 1, 1, 1, 21, 47, 47, 21, 21, 21, 21, 21, 21, 21, 21, 1, 21, 21] 47 rigid atoms, others: [12, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33]) total number of confs: 139 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042107 none NC(=O)C(=O)N1CC2(C1)CCN(C(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [15, 5, 15, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 21, 21, 21, 21, 21, 1, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 21, 1, 1] 47 rigid atoms, others: [32, 33, 3, 5, 6, 7, 8, 9, 10, 11, 12, 20, 23, 24, 25, 26, 27, 28, 29, 30] set([0, 1, 2, 4, 13, 14, 15, 16, 17, 18, 19, 21, 22, 31]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042107 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042107 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042107/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042107 Building REAL250005042108 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042108' /scratch/stefan/7921153/working/building/REAL250005042108 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042108 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042108/0 /scratch/stefan/7921153/working/building/REAL250005042108 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 217) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/217 `/scratch/stefan/7921153/working/3D/217' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC(=O)N1CC2(C1)CCN(C(=O)C1=CC(=O)[N-]O1)C2) `REAL250005042108.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042108/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042108 none C=CCC(=O)N1CC2(C1)CCN(C(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 45, 24, 45, 24, 24, 24, 24, 24, 24, 9, 1, 9, 1, 1, 1, 1, 1, 1, 24, 76, 76, 76, 76, 76, 24, 24, 24, 24, 24, 24, 24, 24, 1, 24, 24] 76 rigid atoms, others: [34, 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, 35, 36]) total number of confs: 259 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042108 none C=CCC(=O)N1CC2(C1)CCN(C(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [42, 25, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 24, 24, 24, 24, 24, 1, 42, 42, 42, 25, 25, 1, 1, 1, 1, 1, 1, 1, 1, 24, 1, 1] 76 rigid atoms, others: [32, 33, 3, 36, 5, 6, 7, 8, 9, 10, 11, 12, 35, 20, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 34, 4, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042108 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042108 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042108/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042108 Building REAL250005042109 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042109' /scratch/stefan/7921153/working/building/REAL250005042109 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042109 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042109/0 /scratch/stefan/7921153/working/building/REAL250005042109 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 218) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/218 `/scratch/stefan/7921153/working/3D/218' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CO)N1CC2(C1)CCN(C(=O)C1=CC(=O)[N-]O1)C2) `REAL250005042109.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042109.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042109/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042109 none O=C(CO)N1CC2(C1)CCN(C(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [39, 23, 39, 45, 23, 23, 23, 23, 23, 23, 9, 1, 9, 1, 1, 1, 1, 1, 1, 23, 45, 45, 135, 23, 23, 23, 23, 23, 23, 23, 23, 1, 23, 23] 135 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 31] 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, 32, 33]) total number of confs: 273 number of broken/clashed sets: 11 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042109 none O=C(CO)N1CC2(C1)CCN(C(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 135 conformations in input total number of sets (complete confs): 135 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 19, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 23, 23, 23, 23, 23, 1, 19, 19, 57, 1, 1, 1, 1, 1, 1, 1, 1, 23, 1, 1] 135 rigid atoms, others: [32, 1, 33, 4, 5, 6, 7, 8, 9, 10, 11, 19, 23, 24, 25, 26, 27, 28, 29, 30] set([0, 2, 3, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 31]) total number of confs: 151 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042109 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042109 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042109/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042109 Building REAL250005042110 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042110' /scratch/stefan/7921153/working/building/REAL250005042110 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042110 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042110/0 /scratch/stefan/7921153/working/building/REAL250005042110 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 219) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/219 `/scratch/stefan/7921153/working/3D/219' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)C(=O)N1CC2(C1)CCN(C(=O)C1=CC(=O)[N-]O1)C2) `REAL250005042110.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042110/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042110 none CC(O)C(=O)N1CC2(C1)CCN(C(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [58, 39, 58, 27, 39, 27, 27, 27, 27, 27, 27, 10, 1, 10, 1, 1, 1, 1, 1, 1, 27, 58, 58, 58, 58, 174, 27, 27, 27, 27, 27, 27, 27, 27, 1, 27, 27] 174 rigid atoms, others: [34, 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, 35, 36]) total number of confs: 360 number of broken/clashed sets: 27 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042110 none CC(O)C(=O)N1CC2(C1)CCN(C(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [21, 6, 21, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 27, 27, 27, 27, 27, 1, 21, 21, 21, 21, 63, 1, 1, 1, 1, 1, 1, 1, 1, 27, 1, 1] 174 rigid atoms, others: [32, 33, 3, 36, 5, 6, 7, 8, 9, 10, 11, 12, 35, 20, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 34, 4, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25]) total number of confs: 169 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042110 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042110 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042110/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042110 Building REAL250005042111 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042111' /scratch/stefan/7921153/working/building/REAL250005042111 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042111 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042111/0 /scratch/stefan/7921153/working/building/REAL250005042111 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 220) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/220 `/scratch/stefan/7921153/working/3D/220' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCF)N1CC2(C1)CCN(C(=O)C1=CC(=O)[N-]O1)C2) `REAL250005042111.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042111/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042111 none O=C(CCF)N1CC2(C1)CCN(C(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'F', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 15, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [35, 21, 35, 77, 77, 21, 21, 21, 21, 21, 21, 8, 1, 8, 1, 1, 1, 1, 1, 1, 21, 77, 77, 77, 77, 21, 21, 21, 21, 21, 21, 21, 21, 1, 21, 21] 77 rigid atoms, others: [33, 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, 34, 35]) total number of confs: 283 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042111 none O=C(CCF)N1CC2(C1)CCN(C(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'F', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 15, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 17, 39, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 21, 21, 21, 21, 21, 1, 18, 18, 38, 38, 1, 1, 1, 1, 1, 1, 1, 1, 21, 1, 1] 77 rigid atoms, others: [32, 1, 34, 35, 5, 6, 7, 8, 9, 10, 11, 12, 20, 25, 26, 27, 28, 29, 30, 31] set([0, 33, 2, 3, 4, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042111 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042111 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042111/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042111 Building REAL250005042112 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042112' /scratch/stefan/7921153/working/building/REAL250005042112 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042112 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042112/0 /scratch/stefan/7921153/working/building/REAL250005042112 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 221) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/221 `/scratch/stefan/7921153/working/3D/221' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](O)C(=O)N1CC2(C1)CCN(C(=O)C1=CC(=O)[N-]O1)C2) `REAL250005042112.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042112/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042112 none C[C@@H](O)C(=O)N1CC2(C1)CCN(C(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 117 conformations in input total number of sets (complete confs): 117 using faster count positions algorithm for large data unique positions, atoms: [39, 26, 39, 39, 17, 26, 17, 17, 17, 17, 17, 17, 8, 1, 8, 1, 1, 1, 1, 1, 1, 17, 39, 39, 39, 117, 17, 17, 17, 17, 17, 17, 17, 17, 1, 17, 17] 117 rigid atoms, others: [34, 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, 35, 36]) total number of confs: 249 number of broken/clashed sets: 20 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042112 none C[C@@H](O)C(=O)N1CC2(C1)CCN(C(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 117 conformations in input total number of sets (complete confs): 117 using faster count positions algorithm for large data unique positions, atoms: [18, 4, 18, 18, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 17, 17, 17, 17, 17, 1, 18, 18, 18, 54, 1, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1] 117 rigid atoms, others: [32, 33, 35, 4, 6, 7, 8, 9, 10, 11, 12, 13, 21, 36, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 34, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25]) total number of confs: 140 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042112 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042112 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042112/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042112 Building REAL250005042113 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042113' /scratch/stefan/7921153/working/building/REAL250005042113 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042113 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042113/0 /scratch/stefan/7921153/working/building/REAL250005042113 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 222) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/222 `/scratch/stefan/7921153/working/3D/222' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](O)C(=O)N1CC2(C1)CCN(C(=O)C1=CC(=O)[N-]O1)C2) `REAL250005042113.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042113/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042113 none C[C@H](O)C(=O)N1CC2(C1)CCN(C(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [41, 27, 41, 41, 18, 27, 18, 18, 18, 18, 18, 18, 9, 1, 9, 1, 1, 1, 1, 1, 1, 18, 41, 41, 41, 123, 18, 18, 18, 18, 18, 18, 18, 18, 1, 18, 18] 123 rigid atoms, others: [34, 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, 35, 36]) total number of confs: 260 number of broken/clashed sets: 20 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042113 none C[C@H](O)C(=O)N1CC2(C1)CCN(C(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [16, 4, 16, 16, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 18, 18, 18, 18, 18, 1, 16, 16, 16, 48, 1, 1, 1, 1, 1, 1, 1, 1, 18, 1, 1] 123 rigid atoms, others: [32, 33, 35, 4, 6, 7, 8, 9, 10, 11, 12, 13, 21, 36, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 34, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25]) total number of confs: 130 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042113 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042113 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042113/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042113 Building REAL250005042114 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042114' /scratch/stefan/7921153/working/building/REAL250005042114 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042114 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042114/0 /scratch/stefan/7921153/working/building/REAL250005042114 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 223) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/223 `/scratch/stefan/7921153/working/3D/223' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=CC(=O)N1CC2(C1)CCN(C(=O)C1=CC(=O)[N-]O1)C2) `REAL250005042114.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042114.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042114/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042114 none CC=CC(=O)N1CC2(C1)CCN(C(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 47, 27, 47, 27, 27, 27, 27, 27, 27, 10, 1, 10, 1, 1, 1, 1, 1, 1, 27, 58, 58, 58, 58, 58, 27, 27, 27, 27, 27, 27, 27, 27, 1, 27, 27] 58 rigid atoms, others: [34, 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, 35, 36]) total number of confs: 156 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042114 none CC=CC(=O)N1CC2(C1)CCN(C(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [20, 20, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 27, 27, 27, 27, 27, 1, 20, 20, 20, 20, 20, 1, 1, 1, 1, 1, 1, 1, 1, 27, 1, 1] 58 rigid atoms, others: [32, 33, 3, 36, 5, 6, 7, 8, 9, 10, 11, 12, 35, 20, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 34, 4, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042114 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042114 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042114/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042114 Building REAL250005042115 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042115' /scratch/stefan/7921153/working/building/REAL250005042115 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042115 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042115/0 /scratch/stefan/7921153/working/building/REAL250005042115 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 224) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/224 `/scratch/stefan/7921153/working/3D/224' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)N1CCC2(CN(C(=O)C3=CC(=O)[N-]O3)C2)C1) `REAL250005042115.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042115.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042115/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042115 none COCC(=O)N1CCC2(CN(C(=O)C3=CC(=O)[N-]O3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [88, 85, 46, 24, 46, 24, 24, 24, 24, 24, 11, 1, 11, 1, 1, 1, 1, 1, 1, 24, 24, 88, 88, 88, 85, 85, 24, 24, 24, 24, 24, 24, 1, 24, 24, 24, 24] 88 rigid atoms, others: [32, 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, 33, 34, 35, 36]) total number of confs: 312 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042115 none COCC(=O)N1CCC2(CN(C(=O)C3=CC(=O)[N-]O3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [41, 22, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 24, 24, 24, 24, 24, 1, 1, 41, 41, 41, 22, 22, 1, 1, 1, 1, 1, 1, 24, 1, 1, 1, 1] 88 rigid atoms, others: [33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 11, 35, 19, 20, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 4, 32, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042115 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042115 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042115/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042115 Building REAL250005042116 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042116' /scratch/stefan/7921153/working/building/REAL250005042116 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042116 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042116/0 /scratch/stefan/7921153/working/building/REAL250005042116 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 225) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/225 `/scratch/stefan/7921153/working/3D/225' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(=O)N1CCC2(CN(C(=O)C3=CC(=O)[N-]O3)C2)C1) `REAL250005042116.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042116.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042116/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042116 none CCCC(=O)N1CCC2(CN(C(=O)C3=CC(=O)[N-]O3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 89, 60, 28, 60, 28, 28, 28, 28, 28, 12, 1, 12, 1, 1, 1, 1, 1, 1, 28, 28, 91, 91, 91, 91, 91, 89, 89, 28, 28, 28, 28, 28, 28, 1, 28, 28, 28, 28] 91 rigid atoms, others: [34, 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, 35, 36, 37, 38]) total number of confs: 310 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042116 none CCCC(=O)N1CCC2(CN(C(=O)C3=CC(=O)[N-]O3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [32, 25, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 28, 28, 28, 28, 28, 1, 1, 36, 36, 36, 35, 35, 25, 25, 1, 1, 1, 1, 1, 1, 28, 1, 1, 1, 1] 91 rigid atoms, others: [32, 33, 3, 36, 5, 6, 7, 8, 9, 10, 11, 35, 37, 19, 20, 38, 28, 29, 30, 31] set([0, 1, 2, 34, 4, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042116 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042116 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042116/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042116 Building REAL250005042117 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042117' /scratch/stefan/7921153/working/building/REAL250005042117 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042117 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042117/0 /scratch/stefan/7921153/working/building/REAL250005042117 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 226) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/226 `/scratch/stefan/7921153/working/3D/226' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N1CCC2(CN(C(=O)C3=CC(=O)[N-]O3)C2)C1) `REAL250005042117.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042117/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042117 none CC(C)C(=O)N1CCC2(CN(C(=O)C3=CC(=O)[N-]O3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 15, 29, 15, 15, 15, 15, 15, 7, 1, 7, 1, 1, 1, 1, 1, 1, 15, 15, 29, 29, 29, 29, 29, 29, 29, 15, 15, 15, 15, 15, 15, 1, 15, 15, 15, 15] 29 rigid atoms, others: [34, 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, 35, 36, 37, 38]) total number of confs: 72 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042117 none CC(C)C(=O)N1CCC2(CN(C(=O)C3=CC(=O)[N-]O3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [9, 7, 9, 1, 7, 1, 1, 1, 1, 1, 1, 1, 6, 6, 15, 15, 15, 15, 15, 1, 1, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1] 29 rigid atoms, others: [32, 33, 3, 36, 5, 6, 7, 8, 9, 10, 11, 35, 37, 19, 20, 38, 28, 29, 30, 31] set([0, 1, 2, 34, 4, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042117 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042117 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042117/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042117 Building REAL250005042118 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042118' /scratch/stefan/7921153/working/building/REAL250005042118 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042118 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042118/0 /scratch/stefan/7921153/working/building/REAL250005042118 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 227) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/227 `/scratch/stefan/7921153/working/3D/227' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N1CCC2(CN(C(=O)C3=CC(=O)[N-]O3)C2)C1) `REAL250005042118.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042118.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042118/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042118 none CCC(=O)N1CCC2(CN(C(=O)C3=CC(=O)[N-]O3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [44, 36, 17, 36, 17, 17, 17, 17, 17, 9, 1, 9, 1, 1, 1, 1, 1, 1, 17, 17, 44, 44, 44, 44, 44, 17, 17, 17, 17, 17, 17, 1, 17, 17, 17, 17] 44 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35]) total number of confs: 143 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042118 none CCC(=O)N1CCC2(CN(C(=O)C3=CC(=O)[N-]O3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [15, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 17, 17, 17, 17, 17, 1, 1, 16, 16, 16, 15, 15, 1, 1, 1, 1, 1, 1, 17, 1, 1, 1, 1] 44 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 10, 34, 18, 19, 25, 26, 27, 28, 29, 30] set([0, 1, 3, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 31]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042118 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042118 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042118/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042118 Building REAL250005042119 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042119' /scratch/stefan/7921153/working/building/REAL250005042119 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042119 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042119/0 /scratch/stefan/7921153/working/building/REAL250005042119 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 228) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/228 `/scratch/stefan/7921153/working/3D/228' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCC2(CN(C(=O)C3=CC(=O)[N-]O3)C2)C1) `REAL250005042119.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042119.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042119/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042119 none CC(=O)N1CCC2(CN(C(=O)C3=CC(=O)[N-]O3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [12, 9, 12, 9, 9, 9, 9, 9, 6, 1, 6, 1, 1, 1, 1, 1, 1, 9, 9, 12, 12, 12, 9, 9, 9, 9, 9, 9, 1, 9, 9, 9, 9] 12 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32]) total number of confs: 31 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042119 none CC(=O)N1CCC2(CN(C(=O)C3=CC(=O)[N-]O3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 9, 9, 9, 9, 9, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 1, 9, 1, 1, 1, 1] 12 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 9, 17, 18, 22, 23, 24, 25, 26, 27, 29, 30, 31] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 28]) total number of confs: 22 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042119 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042119 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042119/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042119 Building REAL250005042120 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042120' /scratch/stefan/7921153/working/building/REAL250005042120 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042120 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042120/0 /scratch/stefan/7921153/working/building/REAL250005042120 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 229) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/229 `/scratch/stefan/7921153/working/3D/229' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(C1=CC(=O)[N-]O1)N1CC2(C1)CCN(C(=O)C1CC1)C2) `REAL250005042120.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042120.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042120/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042120 none O=C(C1=CC(=O)[N-]O1)N1CC2(C1)CCN(C(=O)C1CC1)C2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [35, 13, 35, 40, 40, 40, 40, 40, 13, 13, 13, 13, 13, 13, 8, 1, 8, 1, 1, 1, 13, 40, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 13, 13] 40 rigid atoms, others: [32, 33, 34, 15, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36]) total number of confs: 100 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: REAL250005042120 none O=C(C1=CC(=O)[N-]O1)N1CC2(C1)CCN(C(=O)C1CC1)C2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 25, 25, 25, 25, 25, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 13, 13, 1, 25, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 1, 1] 40 rigid atoms, others: [1, 35, 36, 8, 9, 10, 11, 12, 13, 14, 15, 20, 22, 23, 24, 25, 26, 27, 28, 29] set([0, 32, 2, 3, 4, 5, 6, 7, 34, 16, 17, 18, 19, 21, 33, 30, 31]) total number of confs: 68 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042120 none O=C(C1=CC(=O)[N-]O1)N1CC2(C1)CCN(C(=O)C1CC1)C2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [10, 1, 1, 1, 1, 1, 1, 1, 10, 25, 25, 25, 26, 26, 26, 26, 34, 34, 40, 40, 26, 1, 26, 26, 25, 25, 26, 26, 26, 25, 40, 40, 40, 40, 40, 26, 26] 40 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 21] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042120 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042120 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042120/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042120 Building REAL250005042121 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042121' /scratch/stefan/7921153/working/building/REAL250005042121 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042121 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042121/0 /scratch/stefan/7921153/working/building/REAL250005042121 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 230) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/230 `/scratch/stefan/7921153/working/3D/230' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C(=O)N1CCC2(CN(C(=O)C3=CC(=O)[N-]O3)C2)C1) `REAL250005042121.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042121.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042121/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042121 none NC(=O)C(=O)N1CCC2(CN(C(=O)C3=CC(=O)[N-]O3)C2)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [53, 33, 53, 17, 33, 17, 17, 17, 17, 17, 9, 1, 9, 1, 1, 1, 1, 1, 1, 17, 17, 53, 53, 17, 17, 17, 17, 17, 17, 1, 17, 17, 17, 17] 53 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33]) total number of confs: 161 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042121 none NC(=O)C(=O)N1CCC2(CN(C(=O)C3=CC(=O)[N-]O3)C2)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [14, 5, 14, 1, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 17, 17, 17, 17, 17, 1, 1, 15, 15, 1, 1, 1, 1, 1, 1, 17, 1, 1, 1, 1] 53 rigid atoms, others: [32, 33, 3, 5, 6, 7, 8, 9, 10, 11, 19, 20, 23, 24, 25, 26, 27, 28, 30, 31] set([0, 1, 2, 4, 12, 13, 14, 15, 16, 17, 18, 21, 22, 29]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042121 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042121 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042121/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042121 Building REAL250005042122 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042122' /scratch/stefan/7921153/working/building/REAL250005042122 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042122 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042122/0 /scratch/stefan/7921153/working/building/REAL250005042122 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 231) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/231 `/scratch/stefan/7921153/working/3D/231' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CO)N1CCC2(CN(C(=O)C3=CC(=O)[N-]O3)C2)C1) `REAL250005042122.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042122.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042122/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042122 none O=C(CO)N1CCC2(CN(C(=O)C3=CC(=O)[N-]O3)C2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 129 conformations in input total number of sets (complete confs): 129 using faster count positions algorithm for large data unique positions, atoms: [40, 23, 40, 43, 23, 23, 23, 23, 23, 12, 1, 12, 1, 1, 1, 1, 1, 1, 23, 23, 43, 43, 129, 23, 23, 23, 23, 23, 23, 1, 23, 23, 23, 23] 129 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33]) total number of confs: 250 number of broken/clashed sets: 12 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042122 none O=C(CO)N1CCC2(CN(C(=O)C3=CC(=O)[N-]O3)C2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 129 conformations in input total number of sets (complete confs): 129 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 16, 1, 1, 1, 1, 1, 1, 1, 6, 6, 23, 23, 23, 23, 23, 1, 1, 16, 16, 48, 1, 1, 1, 1, 1, 1, 23, 1, 1, 1, 1] 129 rigid atoms, others: [32, 1, 33, 4, 5, 6, 7, 8, 9, 10, 18, 19, 23, 24, 25, 26, 27, 28, 30, 31] set([0, 2, 3, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 29]) total number of confs: 132 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042122 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042122 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042122/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042122 Building REAL250005042123 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042123' /scratch/stefan/7921153/working/building/REAL250005042123 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042123 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042123/0 /scratch/stefan/7921153/working/building/REAL250005042123 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 232) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/232 `/scratch/stefan/7921153/working/3D/232' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)C(=O)N1CCC2(CN(C(=O)C3=CC(=O)[N-]O3)C2)C1) `REAL250005042123.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042123.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042123/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042123 none CC(O)C(=O)N1CCC2(CN(C(=O)C3=CC(=O)[N-]O3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 87 conformations in input total number of sets (complete confs): 87 using faster count positions algorithm for large data unique positions, atoms: [29, 21, 29, 17, 21, 17, 17, 17, 17, 17, 10, 1, 10, 1, 1, 1, 1, 1, 1, 17, 17, 29, 29, 29, 29, 87, 17, 17, 17, 17, 17, 17, 1, 17, 17, 17, 17] 87 rigid atoms, others: [32, 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, 33, 34, 35, 36]) total number of confs: 172 number of broken/clashed sets: 17 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042123 none CC(O)C(=O)N1CCC2(CN(C(=O)C3=CC(=O)[N-]O3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [12, 5, 12, 1, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 17, 17, 17, 17, 17, 1, 1, 12, 12, 12, 12, 36, 1, 1, 1, 1, 1, 1, 17, 1, 1, 1, 1] 87 rigid atoms, others: [33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 11, 35, 19, 20, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 4, 32, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25]) total number of confs: 100 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042123 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042123 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042123/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042123 Building REAL250005042124 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042124' /scratch/stefan/7921153/working/building/REAL250005042124 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042124 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042124/0 /scratch/stefan/7921153/working/building/REAL250005042124 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 233) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/233 `/scratch/stefan/7921153/working/3D/233' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)C(=O)N1CCC2(CN(C(=O)C3=CC(=O)[N-]O3)C2)C1) `REAL250005042124.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042124/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042124 none CC(=O)C(=O)N1CCC2(CN(C(=O)C3=CC(=O)[N-]O3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [53, 35, 53, 18, 35, 18, 18, 18, 18, 18, 9, 1, 9, 1, 1, 1, 1, 1, 1, 18, 18, 53, 53, 53, 18, 18, 18, 18, 18, 18, 1, 18, 18, 18, 18] 53 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34]) total number of confs: 161 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042124 none CC(=O)C(=O)N1CCC2(CN(C(=O)C3=CC(=O)[N-]O3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [15, 5, 15, 1, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 18, 18, 18, 18, 18, 1, 1, 16, 16, 16, 1, 1, 1, 1, 1, 1, 18, 1, 1, 1, 1] 53 rigid atoms, others: [32, 33, 34, 3, 5, 6, 7, 8, 9, 10, 11, 19, 20, 24, 25, 26, 27, 28, 29, 31] set([0, 1, 2, 4, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 30]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042124 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042124 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042124/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042124 Building REAL250005042125 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042125' /scratch/stefan/7921153/working/building/REAL250005042125 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042125 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042125/0 /scratch/stefan/7921153/working/building/REAL250005042125 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 234) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/234 `/scratch/stefan/7921153/working/3D/234' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=CC(=O)N1CCC2(CN(C(=O)C3=CC(=O)[N-]O3)C2)C1) `REAL250005042125.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042125/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042125 none CC=CC(=O)N1CCC2(CN(C(=O)C3=CC(=O)[N-]O3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 35, 22, 35, 22, 22, 22, 22, 22, 8, 1, 8, 1, 1, 1, 1, 1, 1, 22, 22, 39, 39, 39, 39, 39, 22, 22, 22, 22, 22, 22, 1, 22, 22, 22, 22] 39 rigid atoms, others: [32, 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, 33, 34, 35, 36]) total number of confs: 97 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042125 none CC=CC(=O)N1CCC2(CN(C(=O)C3=CC(=O)[N-]O3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [21, 20, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 6, 6, 22, 22, 22, 22, 22, 1, 1, 21, 21, 21, 21, 21, 1, 1, 1, 1, 1, 1, 22, 1, 1, 1, 1] 39 rigid atoms, others: [33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 11, 35, 19, 20, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 4, 32, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042125 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042125 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042125/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042125 Building REAL250005042126 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042126' /scratch/stefan/7921153/working/building/REAL250005042126 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042126 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042126/0 /scratch/stefan/7921153/working/building/REAL250005042126 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 235) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/235 `/scratch/stefan/7921153/working/3D/235' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](O)C(=O)N1CCC2(CN(C(=O)C3=CC(=O)[N-]O3)C2)C1) `REAL250005042126.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042126.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042126/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042126 none C[C@H](O)C(=O)N1CCC2(CN(C(=O)C3=CC(=O)[N-]O3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [27, 18, 27, 27, 14, 18, 14, 14, 14, 14, 14, 7, 1, 7, 1, 1, 1, 1, 1, 1, 14, 14, 27, 27, 27, 81, 14, 14, 14, 14, 14, 14, 1, 14, 14, 14, 14] 81 rigid atoms, others: [32, 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, 33, 34, 35, 36]) total number of confs: 165 number of broken/clashed sets: 12 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042126 none C[C@H](O)C(=O)N1CCC2(CN(C(=O)C3=CC(=O)[N-]O3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [10, 2, 10, 10, 1, 2, 1, 1, 1, 1, 1, 1, 1, 6, 6, 14, 14, 14, 14, 14, 1, 1, 10, 10, 10, 30, 1, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1] 81 rigid atoms, others: [33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 12, 20, 21, 36, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 32, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25]) total number of confs: 87 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042126 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042126 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042126/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042126 Building REAL250005042127 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042127' /scratch/stefan/7921153/working/building/REAL250005042127 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042127 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042127/0 /scratch/stefan/7921153/working/building/REAL250005042127 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 236) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/236 `/scratch/stefan/7921153/working/3D/236' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC(=O)N1CCC2(CN(C(=O)C3=CC(=O)[N-]O3)C2)C1) `REAL250005042127.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042127/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042127 none C=CCC(=O)N1CCC2(CN(C(=O)C3=CC(=O)[N-]O3)C2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [99, 99, 68, 29, 68, 29, 29, 29, 29, 29, 12, 1, 12, 1, 1, 1, 1, 1, 1, 29, 29, 99, 99, 99, 99, 99, 29, 29, 29, 29, 29, 29, 1, 29, 29, 29, 29] 99 rigid atoms, others: [32, 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, 33, 34, 35, 36]) total number of confs: 338 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042127 none C=CCC(=O)N1CCC2(CN(C(=O)C3=CC(=O)[N-]O3)C2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [64, 29, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 29, 29, 29, 29, 29, 1, 1, 64, 64, 64, 29, 29, 1, 1, 1, 1, 1, 1, 29, 1, 1, 1, 1] 99 rigid atoms, others: [33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 11, 35, 19, 20, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 4, 32, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25]) total number of confs: 249 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042127 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042127 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042127/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042127 Building REAL250005042128 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042128' /scratch/stefan/7921153/working/building/REAL250005042128 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042128 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042128/0 /scratch/stefan/7921153/working/building/REAL250005042128 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 237) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/237 `/scratch/stefan/7921153/working/3D/237' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CCC(=O)N1CCC2(CN(C(=O)C3=CC(=O)[N-]O3)C2)C1) `REAL250005042128.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042128.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042128/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042128 none N#CCC(=O)N1CCC2(CN(C(=O)C3=CC(=O)[N-]O3)C2)C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [64, 64, 32, 19, 32, 19, 19, 19, 19, 19, 9, 1, 9, 1, 1, 1, 1, 1, 1, 19, 19, 64, 64, 19, 19, 19, 19, 19, 19, 1, 19, 19, 19, 19] 64 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33]) total number of confs: 220 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042128 none N#CCC(=O)N1CCC2(CN(C(=O)C3=CC(=O)[N-]O3)C2)C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [23, 23, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 5, 5, 19, 19, 19, 19, 19, 1, 1, 23, 23, 1, 1, 1, 1, 1, 1, 19, 1, 1, 1, 1] 64 rigid atoms, others: [32, 33, 3, 5, 6, 7, 8, 9, 10, 11, 19, 20, 23, 24, 25, 26, 27, 28, 30, 31] set([0, 1, 2, 4, 12, 13, 14, 15, 16, 17, 18, 21, 22, 29]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042128 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042128 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042128/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042128 Building REAL250005042129 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042129' /scratch/stefan/7921153/working/building/REAL250005042129 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042129 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042129/0 /scratch/stefan/7921153/working/building/REAL250005042129 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 238) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/238 `/scratch/stefan/7921153/working/3D/238' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCF)N1CCC2(CN(C(=O)C3=CC(=O)[N-]O3)C2)C1) `REAL250005042129.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042129/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042129 none O=C(CCF)N1CCC2(CN(C(=O)C3=CC(=O)[N-]O3)C2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'F', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 15, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [44, 26, 44, 70, 70, 26, 26, 26, 26, 26, 10, 1, 10, 1, 1, 1, 1, 1, 1, 26, 26, 70, 70, 70, 70, 26, 26, 26, 26, 26, 26, 1, 26, 26, 26, 26] 70 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 31] 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, 32, 33, 34, 35]) total number of confs: 226 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042129 none O=C(CCF)N1CCC2(CN(C(=O)C3=CC(=O)[N-]O3)C2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'F', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 15, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [5, 1, 5, 21, 36, 1, 1, 1, 1, 1, 1, 1, 6, 6, 26, 26, 26, 26, 26, 1, 1, 21, 21, 36, 36, 1, 1, 1, 1, 1, 1, 26, 1, 1, 1, 1] 70 rigid atoms, others: [32, 1, 34, 33, 5, 6, 7, 8, 9, 10, 11, 19, 20, 25, 26, 27, 28, 29, 30, 35] set([0, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 31]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042129 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042129 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042129/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042129 Building REAL250005042130 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042130' /scratch/stefan/7921153/working/building/REAL250005042130 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042130 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042130/0 /scratch/stefan/7921153/working/building/REAL250005042130 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 239) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/239 `/scratch/stefan/7921153/working/3D/239' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](O)C(=O)N1CCC2(CN(C(=O)C3=CC(=O)[N-]O3)C2)C1) `REAL250005042130.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042130/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042130 none C[C@@H](O)C(=O)N1CCC2(CN(C(=O)C3=CC(=O)[N-]O3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [30, 22, 30, 30, 18, 22, 18, 18, 18, 18, 17, 7, 1, 7, 1, 1, 1, 1, 1, 1, 18, 18, 30, 30, 30, 90, 18, 18, 18, 18, 17, 17, 1, 18, 18, 18, 18] 90 rigid atoms, others: [32, 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, 33, 34, 35, 36]) total number of confs: 177 number of broken/clashed sets: 14 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042130 none C[C@@H](O)C(=O)N1CCC2(CN(C(=O)C3=CC(=O)[N-]O3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [10, 4, 10, 10, 1, 4, 1, 1, 1, 1, 1, 1, 1, 6, 6, 17, 17, 17, 17, 17, 1, 1, 10, 10, 10, 30, 1, 1, 1, 1, 1, 1, 18, 1, 1, 1, 1] 90 rigid atoms, others: [33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 12, 20, 21, 36, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 32, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25]) total number of confs: 93 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042130 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042130 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042130/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042130 Building REAL250005042131 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042131' /scratch/stefan/7921153/working/building/REAL250005042131 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042131 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042131/0 /scratch/stefan/7921153/working/building/REAL250005042131 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 240) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/240 `/scratch/stefan/7921153/working/3D/240' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(=O)N1CCC2(CN(C(=O)C3=CC(=O)[N-]O3)C2)C1) `REAL250005042131.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042131/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042131 none C=CC(=O)N1CCC2(CN(C(=O)C3=CC(=O)[N-]O3)C2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 20, 36, 20, 20, 20, 20, 20, 10, 1, 10, 1, 1, 1, 1, 1, 1, 20, 20, 36, 36, 36, 20, 20, 20, 20, 20, 20, 1, 20, 20, 20, 20] 36 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33]) total number of confs: 87 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042131 none C=CC(=O)N1CCC2(CN(C(=O)C3=CC(=O)[N-]O3)C2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [16, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 20, 20, 20, 20, 20, 1, 1, 16, 16, 16, 1, 1, 1, 1, 1, 1, 20, 1, 1, 1, 1] 36 rigid atoms, others: [32, 33, 2, 4, 5, 6, 7, 8, 9, 10, 18, 19, 23, 24, 25, 26, 27, 28, 30, 31] set([0, 1, 3, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 29]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042131 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042131 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042131/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042131 Building REAL250005042132 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042132' /scratch/stefan/7921153/working/building/REAL250005042132 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042132 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042132/0 /scratch/stefan/7921153/working/building/REAL250005042132 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 241) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/241 `/scratch/stefan/7921153/working/3D/241' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)NCC1CN(C(=O)C2=CC(=O)[N-]O2)CCCO1) `REAL250005042132.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042132.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042132/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042132 none CCC(=O)NCC1CN(C(=O)C2=CC(=O)[N-]O2)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 12, 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, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 41, 41, 41, 30, 11, 11, 11, 6, 1, 6, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 59, 59, 59, 59, 59, 41, 30, 30, 11, 11, 11, 1, 11, 11, 11, 11, 11, 11] 59 rigid atoms, others: [32, 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, 33, 34, 35, 36, 37, 38]) total number of confs: 248 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042132 none CCC(=O)NCC1CN(C(=O)C2=CC(=O)[N-]O2)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 12, 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, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [40, 22, 22, 22, 7, 1, 1, 1, 1, 1, 6, 6, 11, 11, 11, 11, 11, 1, 1, 1, 1, 40, 40, 40, 40, 40, 22, 7, 7, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1] 59 rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 38, 17, 18, 19, 20, 37, 29, 30, 31] set([0, 1, 2, 3, 4, 32, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042132 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042132 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042132/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042132 Building REAL250005042133 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042133' /scratch/stefan/7921153/working/building/REAL250005042133 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042133 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042133/0 /scratch/stefan/7921153/working/building/REAL250005042133 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 242) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/242 `/scratch/stefan/7921153/working/3D/242' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC1CN(C(=O)C2=CC(=O)[N-]O2)CCCO1) `REAL250005042133.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042133/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042133 none CC(=O)NCC1CN(C(=O)C2=CC(=O)[N-]O2)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 33, 14, 14, 14, 7, 1, 7, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 36, 36, 36, 36, 33, 33, 14, 14, 14, 1, 14, 14, 14, 14, 14, 14] 36 rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35]) total number of confs: 119 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042133 none CC(=O)NCC1CN(C(=O)C2=CC(=O)[N-]O2)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [18, 18, 18, 7, 1, 1, 1, 1, 1, 7, 7, 14, 14, 14, 14, 14, 1, 1, 1, 1, 19, 19, 19, 18, 7, 7, 1, 1, 1, 14, 1, 1, 1, 1, 1, 1] 36 rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 16, 17, 18, 19, 26, 27, 28, 30, 31] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 29]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042133 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042133 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042133/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042133 Building REAL250005042134 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042134' /scratch/stefan/7921153/working/building/REAL250005042134 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042134 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042134/0 /scratch/stefan/7921153/working/building/REAL250005042134 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 243) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/243 `/scratch/stefan/7921153/working/3D/243' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CO)NCC1CN(C(=O)C2=CC(=O)[N-]O2)CCCO1) `REAL250005042134.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042134.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042134/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042134 none O=C(CO)NCC1CN(C(=O)C2=CC(=O)[N-]O2)CCCO1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 12, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 408 conformations in input total number of sets (complete confs): 408 using faster count positions algorithm for large data unique positions, atoms: [135, 135, 135, 136, 90, 28, 28, 28, 11, 1, 11, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 136, 136, 408, 135, 90, 90, 28, 28, 28, 1, 28, 28, 28, 28, 28, 28] 408 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36]) total number of confs: 873 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042134 none O=C(CO)NCC1CN(C(=O)C2=CC(=O)[N-]O2)CCCO1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 12, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 408 conformations in input total number of sets (complete confs): 408 using faster count positions algorithm for large data unique positions, atoms: [45, 45, 45, 86, 9, 1, 1, 1, 1, 1, 7, 7, 28, 28, 28, 28, 28, 1, 1, 1, 1, 86, 86, 258, 45, 9, 9, 1, 1, 1, 28, 1, 1, 1, 1, 1, 1] 408 rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 17, 18, 19, 20, 27, 28, 29, 31] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 30]) total number of confs: 610 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042134 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042134 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042134/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042134 Building REAL250005042135 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042135' /scratch/stefan/7921153/working/building/REAL250005042135 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042135 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042135/0 /scratch/stefan/7921153/working/building/REAL250005042135 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 244) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/244 `/scratch/stefan/7921153/working/3D/244' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N1CCCOC(CNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042135.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042135.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042135/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042135 none CCC(=O)N1CCCOC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 70, 108, 70, 70, 70, 70, 70, 31, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 70, 108, 108, 108, 108, 108, 70, 70, 70, 70, 70, 70, 70, 31, 31, 8, 1, 70, 70] 108 rigid atoms, others: [36, 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, 37, 38]) total number of confs: 331 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042135 none CCC(=O)N1CCCOC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [16, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 10, 49, 49, 49, 70, 70, 70, 70, 70, 1, 17, 17, 17, 16, 16, 1, 1, 1, 1, 1, 1, 1, 10, 10, 49, 70, 1, 1] 108 rigid atoms, others: [32, 2, 4, 5, 6, 7, 8, 9, 10, 38, 37, 20, 26, 27, 28, 29, 30, 31] set([0, 1, 34, 3, 36, 35, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25]) total number of confs: 226 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042135 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042135 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042135/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042135 Building REAL250005042136 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042136' /scratch/stefan/7921153/working/building/REAL250005042136 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042136 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042136/0 /scratch/stefan/7921153/working/building/REAL250005042136 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 245) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/245 `/scratch/stefan/7921153/working/3D/245' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCCOC(CNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042136.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042136/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042136 none CC(=O)N1CCCOC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [47, 36, 47, 36, 36, 36, 36, 36, 18, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 36, 47, 47, 47, 36, 36, 36, 36, 36, 36, 36, 17, 17, 8, 1, 36, 36] 47 rigid atoms, others: [33, 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, 34, 35]) total number of confs: 157 number of broken/clashed sets: 26 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042136 none CC(=O)N1CCCOC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 10, 32, 32, 32, 36, 36, 36, 36, 36, 1, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 10, 10, 32, 36, 1, 1] 47 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 8, 9, 19, 23, 24, 25, 26, 27, 28, 29, 35] set([0, 32, 2, 33, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 30, 31]) total number of confs: 110 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042136 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042136 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042136/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042136 Building REAL250005042137 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042137' /scratch/stefan/7921153/working/building/REAL250005042137 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042137 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042137/0 /scratch/stefan/7921153/working/building/REAL250005042137 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 246) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/246 `/scratch/stefan/7921153/working/3D/246' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CO)N1CCCOC(CNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042137.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042137/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042137 none O=C(CO)N1CCCOC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 5, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 195 conformations in input total number of sets (complete confs): 195 using faster count positions algorithm for large data unique positions, atoms: [57, 48, 57, 65, 48, 48, 48, 48, 48, 23, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 48, 65, 65, 195, 48, 48, 48, 48, 48, 48, 48, 23, 23, 8, 1, 48, 48] 195 rigid atoms, others: [34, 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, 35, 36]) total number of confs: 423 number of broken/clashed sets: 32 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042137 none O=C(CO)N1CCCOC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 5, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 195 conformations in input total number of sets (complete confs): 195 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 19, 1, 1, 1, 1, 1, 1, 1, 10, 37, 37, 37, 48, 48, 48, 48, 48, 1, 19, 19, 57, 1, 1, 1, 1, 1, 1, 1, 10, 10, 37, 48, 1, 1] 195 rigid atoms, others: [1, 35, 4, 5, 6, 7, 8, 9, 10, 20, 24, 25, 26, 27, 28, 29, 30, 36] set([0, 32, 2, 3, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 34, 31]) total number of confs: 246 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042137 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042137 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042137/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042137 Building REAL250005042138 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042138' /scratch/stefan/7921153/working/building/REAL250005042138 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042138 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042138/0 /scratch/stefan/7921153/working/building/REAL250005042138 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 247) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/247 `/scratch/stefan/7921153/working/3D/247' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(=O)N1CCCOC(CNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042138.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042138.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042138/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042138 none C=CC(=O)N1CCCOC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 5, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 51, 72, 51, 51, 51, 51, 51, 18, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 51, 72, 72, 72, 51, 51, 51, 51, 51, 51, 51, 17, 17, 6, 1, 51, 51] 72 rigid atoms, others: [34, 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, 35, 36]) total number of confs: 226 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042138 none C=CC(=O)N1CCCOC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 5, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [22, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 9, 40, 40, 40, 50, 50, 50, 50, 51, 1, 22, 22, 22, 1, 1, 1, 1, 1, 1, 1, 9, 9, 40, 51, 1, 1] 72 rigid atoms, others: [2, 35, 4, 5, 6, 7, 8, 9, 10, 20, 24, 25, 26, 27, 28, 29, 30, 36] set([0, 1, 34, 3, 33, 32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 31]) total number of confs: 182 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042138 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042138 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042138/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042138 Building REAL250005042139 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042139' /scratch/stefan/7921153/working/building/REAL250005042139 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042139 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042139/0 /scratch/stefan/7921153/working/building/REAL250005042139 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 248) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/248 `/scratch/stefan/7921153/working/3D/248' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)NC[C@@H](C)N(CC)C(=O)C1=CC(=O)[N-]O1) `REAL250005042139.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042139.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042139/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042139 none CCC(=O)NC[C@@H](C)N(CC)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 7, 5, 8, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 139, 139, 139, 91, 49, 27, 49, 49, 8, 27, 36, 1, 8, 1, 1, 1, 1, 1, 1, 191, 191, 191, 191, 191, 139, 91, 91, 49, 49, 49, 36, 36, 36, 36, 36, 1] 201 rigid atoms, others: [36, 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]) total number of confs: 885 number of broken/clashed sets: 124 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042139 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042139 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042139/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042139 Building REAL250005042140 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042140' /scratch/stefan/7921153/working/building/REAL250005042140 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042140 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042140/0 /scratch/stefan/7921153/working/building/REAL250005042140 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 249) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/249 `/scratch/stefan/7921153/working/3D/249' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C1=CC(=O)[N-]O1)[C@H](C)CNC(=O)CCOC) `REAL250005042140.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042140/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042140 none CCN(C(=O)C1=CC(=O)[N-]O1)[C@H](C)CNC(=O)CCOC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 8, 1, 11, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 17, 7, 1, 7, 1, 1, 1, 1, 1, 1, 17, 27, 27, 27, 54, 84, 84, 84, 176, 191, 193, 22, 22, 22, 22, 22, 1, 27, 27, 27, 54, 54, 84, 176, 176, 191, 191, 193, 193, 193] 201 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 27] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 853 number of broken/clashed sets: 121 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042140 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042140 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042140/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042140 Building REAL250005042141 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042141' /scratch/stefan/7921153/working/building/REAL250005042141 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042141 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042141/0 /scratch/stefan/7921153/working/building/REAL250005042141 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 250) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/250 `/scratch/stefan/7921153/working/3D/250' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C1=CC(=O)[N-]O1)[C@H](C)CNC(C)=O) `REAL250005042141.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042141/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042141 none CCN(C(=O)C1=CC(=O)[N-]O1)[C@H](C)CNC(C)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 8, 1, 5, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 52 conformations in input total number of sets (complete confs): 52 using faster count positions algorithm for large data unique positions, atoms: [19, 15, 7, 1, 7, 1, 1, 1, 1, 1, 1, 15, 25, 25, 25, 37, 51, 51, 51, 19, 19, 19, 19, 19, 1, 25, 25, 25, 37, 37, 51, 51, 51, 51] 52 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 24] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 213 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042141 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042141 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042141/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042141 Building REAL250005042142 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042142' /scratch/stefan/7921153/working/building/REAL250005042142 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042142 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042142/0 /scratch/stefan/7921153/working/building/REAL250005042142 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 251) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/251 `/scratch/stefan/7921153/working/3D/251' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C1=CC(=O)[N-]O1)[C@H](C)CNC(=O)C1CC1) `REAL250005042142.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042142/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042142 none CCN(C(=O)C1=CC(=O)[N-]O1)[C@H](C)CNC(=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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] 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: [105, 80, 64, 80, 104, 104, 168, 168, 168, 168, 168, 39, 64, 64, 10, 10, 1, 10, 1, 1, 1, 105, 105, 105, 105, 105, 168, 64, 64, 64, 39, 39, 10, 1, 1, 1, 1, 1] 168 rigid atoms, others: [33, 34, 35, 36, 37, 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]) total number of confs: 651 number of broken/clashed sets: 31 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042142 none CCN(C(=O)C1=CC(=O)[N-]O1)[C@H](C)CNC(=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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] 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: [18, 15, 8, 1, 8, 1, 1, 1, 1, 1, 1, 15, 26, 26, 26, 46, 80, 80, 80, 166, 166, 18, 18, 18, 18, 18, 1, 26, 26, 26, 46, 46, 80, 166, 166, 166, 166, 166] 166 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 26] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 546 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042142 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042142 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042142/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042142 Building REAL250005042143 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042143' /scratch/stefan/7921153/working/building/REAL250005042143 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042143 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042143/0 /scratch/stefan/7921153/working/building/REAL250005042143 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 252) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/252 `/scratch/stefan/7921153/working/3D/252' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C1=CC(=O)[N-]O1)[C@H](C)CNC(=O)C1CCC1) `REAL250005042143.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042143/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042143 none CCN(C(=O)C1=CC(=O)[N-]O1)[C@H](C)CNC(=O)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [127, 98, 79, 98, 139, 139, 192, 192, 192, 192, 192, 41, 79, 79, 10, 10, 1, 10, 1, 1, 1, 1, 127, 127, 127, 127, 127, 192, 79, 79, 79, 41, 41, 10, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 16, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 803 number of broken/clashed sets: 121 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042143 none CCN(C(=O)C1=CC(=O)[N-]O1)[C@H](C)CNC(=O)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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, 7, 7, 7] 0 hydrogens 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, 22, 8, 1, 8, 1, 1, 1, 1, 1, 1, 22, 36, 36, 36, 66, 93, 93, 93, 192, 192, 192, 30, 30, 30, 30, 30, 1, 36, 36, 36, 66, 66, 93, 192, 192, 192, 192, 192, 192, 192] 201 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 27] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 722 number of broken/clashed sets: 121 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042143 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042143 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042143/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042143 Building REAL250005042144 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042144' /scratch/stefan/7921153/working/building/REAL250005042144 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042144 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042144/0 /scratch/stefan/7921153/working/building/REAL250005042144 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 253) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/253 `/scratch/stefan/7921153/working/3D/253' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C1=CC(=O)[N-]O1)[C@H](C)CNC(=O)CC1CC1) `REAL250005042144.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042144/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042144 none CCN(C(=O)C1=CC(=O)[N-]O1)[C@H](C)CNC(=O)CC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [149, 125, 108, 125, 162, 162, 192, 192, 192, 192, 192, 76, 108, 108, 22, 22, 3, 22, 1, 1, 1, 1, 149, 149, 149, 149, 149, 192, 108, 108, 108, 76, 76, 22, 3, 3, 1, 1, 1, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 40, 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]) total number of confs: 862 number of broken/clashed sets: 118 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042144 none CCN(C(=O)C1=CC(=O)[N-]O1)[C@H](C)CNC(=O)CC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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, 7, 7, 7] 0 hydrogens 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, 19, 8, 1, 8, 1, 1, 1, 1, 1, 1, 19, 28, 28, 28, 52, 78, 78, 78, 154, 192, 192, 25, 25, 25, 25, 25, 1, 28, 28, 28, 52, 52, 78, 154, 154, 192, 192, 192, 192, 192] 201 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 27] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 863 number of broken/clashed sets: 118 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042144 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042144 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042144/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042144 Building REAL250005042145 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042145' /scratch/stefan/7921153/working/building/REAL250005042145 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042145 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042145/0 /scratch/stefan/7921153/working/building/REAL250005042145 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 254) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/254 `/scratch/stefan/7921153/working/3D/254' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C1=CC(=O)[N-]O1)[C@H](C)CNC(=O)COC) `REAL250005042145.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042145/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042145 none CCN(C(=O)C1=CC(=O)[N-]O1)[C@H](C)CNC(=O)COC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [19, 16, 7, 1, 7, 1, 1, 1, 1, 1, 1, 16, 18, 18, 18, 25, 42, 42, 42, 80, 87, 19, 19, 19, 19, 19, 1, 18, 18, 18, 25, 25, 42, 80, 80, 87, 87, 87] 90 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 26] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 354 number of broken/clashed sets: 61 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042145 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042145 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042145/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042145 Building REAL250005042146 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042146' /scratch/stefan/7921153/working/building/REAL250005042146 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042146 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042146/0 /scratch/stefan/7921153/working/building/REAL250005042146 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 255) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/255 `/scratch/stefan/7921153/working/3D/255' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(=O)NC[C@@H](C)N(CC)C(=O)C1=CC(=O)[N-]O1) `REAL250005042146.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042146/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042146 none CCCC(=O)NC[C@@H](C)N(CC)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 8, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 178, 85, 85, 85, 52, 30, 20, 30, 30, 8, 20, 27, 1, 8, 1, 1, 1, 1, 1, 1, 193, 193, 193, 193, 193, 178, 178, 85, 52, 52, 30, 30, 30, 27, 27, 27, 27, 27, 1] 201 rigid atoms, others: [39, 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]) total number of confs: 899 number of broken/clashed sets: 123 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042146 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042146 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042146/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042146 Building REAL250005042147 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042147' /scratch/stefan/7921153/working/building/REAL250005042147 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042147 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042147/0 /scratch/stefan/7921153/working/building/REAL250005042147 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 256) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/256 `/scratch/stefan/7921153/working/3D/256' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C1=CC(=O)[N-]O1)[C@H](C)CNC(=O)CC(C)C) `REAL250005042147.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042147/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042147 none CCN(C(=O)C1=CC(=O)[N-]O1)[C@H](C)CNC(=O)CC(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 8, 1, 8, 1, 1, 1, 1, 1, 1, 20, 38, 38, 38, 72, 123, 123, 123, 190, 191, 191, 29, 29, 29, 29, 29, 1, 38, 38, 38, 72, 72, 123, 190, 190, 191, 191, 191, 191, 191, 191, 191] 201 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 27] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 857 number of broken/clashed sets: 124 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042147 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042147 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042147/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042147 Building REAL250005042148 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042148' /scratch/stefan/7921153/working/building/REAL250005042148 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042148 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042148/0 /scratch/stefan/7921153/working/building/REAL250005042148 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 257) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/257 `/scratch/stefan/7921153/working/3D/257' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C1=CC(=O)[N-]O1)[C@H](C)CNC(=O)C1CC1C) `REAL250005042148.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042148.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042148/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042148 none CCN(C(=O)C1=CC(=O)[N-]O1)[C@H](C)CNC(=O)C1CC1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [134, 107, 87, 107, 153, 153, 192, 192, 192, 192, 192, 47, 87, 87, 12, 12, 1, 12, 1, 1, 1, 1, 134, 134, 134, 134, 134, 192, 87, 87, 87, 47, 47, 12, 1, 1, 1, 1, 2, 2, 2] 201 rigid atoms, others: [34, 35, 36, 37, 16, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40]) total number of confs: 830 number of broken/clashed sets: 123 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042148 none CCN(C(=O)C1=CC(=O)[N-]O1)[C@H](C)CNC(=O)C1CC1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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, 7, 7, 7] 0 hydrogens 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, 20, 8, 1, 8, 1, 1, 1, 1, 1, 1, 20, 36, 36, 36, 69, 103, 103, 103, 192, 192, 192, 31, 31, 31, 31, 31, 1, 36, 36, 36, 69, 69, 103, 192, 192, 192, 192, 192, 192, 192] 201 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 27] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 764 number of broken/clashed sets: 123 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042148 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042148 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042148/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042148 Building REAL250005042149 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042149' /scratch/stefan/7921153/working/building/REAL250005042149 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042149 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042149/0 /scratch/stefan/7921153/working/building/REAL250005042149 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 258) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/258 `/scratch/stefan/7921153/working/3D/258' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCC(=O)NC[C@@H](C)N(CC)C(=O)C1=CC(=O)[N-]O1) `REAL250005042149.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042149.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042149/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042149 none CCOCC(=O)NC[C@@H](C)N(CC)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 5, 7, 5, 8, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [124, 124, 121, 83, 83, 83, 49, 27, 17, 27, 27, 7, 17, 22, 1, 7, 1, 1, 1, 1, 1, 1, 124, 124, 124, 124, 124, 122, 122, 83, 49, 49, 27, 27, 27, 22, 22, 22, 22, 22, 1] 140 rigid atoms, others: [40, 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]) total number of confs: 542 number of broken/clashed sets: 123 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042149 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042149 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042149/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042149 Building REAL250005042150 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042150' /scratch/stefan/7921153/working/building/REAL250005042150 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042150 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042150/0 /scratch/stefan/7921153/working/building/REAL250005042150 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 259) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/259 `/scratch/stefan/7921153/working/3D/259' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C1=CC(=O)[N-]O1)[C@H](C)CNC(=O)C=C(C)C) `REAL250005042150.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042150.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042150/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042150 none CCN(C(=O)C1=CC(=O)[N-]O1)[C@H](C)CNC(=O)C=C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 8, 1, 11, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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, 7, 7, 7] 0 hydrogens 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, 22, 8, 1, 8, 1, 1, 1, 1, 1, 1, 22, 36, 36, 36, 68, 111, 111, 111, 185, 185, 185, 31, 31, 31, 31, 31, 1, 36, 36, 36, 68, 68, 111, 185, 185, 185, 185, 185, 185, 185] 201 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 27] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 739 number of broken/clashed sets: 119 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042150 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042150 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042150/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042150 Building REAL250005042151 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042151' /scratch/stefan/7921153/working/building/REAL250005042151 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042151 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042151/0 /scratch/stefan/7921153/working/building/REAL250005042151 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 260) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/260 `/scratch/stefan/7921153/working/3D/260' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCC(=O)NC[C@@H](C)N(CC)C(=O)C1=CC(=O)[N-]O1) `REAL250005042151.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042151.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042151/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042151 none CCCCC(=O)NC[C@@H](C)N(CC)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 8, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [94, 94, 86, 29, 29, 29, 25, 19, 15, 19, 19, 6, 15, 18, 1, 6, 1, 1, 1, 1, 1, 1, 94, 94, 94, 94, 94, 94, 94, 86, 86, 29, 25, 25, 19, 19, 19, 18, 18, 18, 18, 18, 1] 100 rigid atoms, others: [42, 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, 41]) total number of confs: 397 number of broken/clashed sets: 99 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042151 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042151 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042151/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042151 Building REAL250005042152 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042152' /scratch/stefan/7921153/working/building/REAL250005042152 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042152 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042152/0 /scratch/stefan/7921153/working/building/REAL250005042152 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 261) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/261 `/scratch/stefan/7921153/working/3D/261' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C1=CC(=O)[N-]O1)[C@H](C)CNC(=O)C(C)C) `REAL250005042152.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042152/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042152 none CCN(C(=O)C1=CC(=O)[N-]O1)[C@H](C)CNC(=O)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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, 7, 7] 0 hydrogens need rotated 155 conformations in input total number of sets (complete confs): 155 using faster count positions algorithm for large data unique positions, atoms: [23, 18, 9, 1, 9, 1, 1, 1, 1, 1, 1, 18, 32, 32, 32, 60, 104, 104, 104, 155, 155, 23, 23, 23, 23, 23, 1, 32, 32, 32, 60, 60, 104, 155, 155, 155, 155, 155, 155, 155] 155 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 26] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 693 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042152 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042152 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042152/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042152 Building REAL250005042153 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042153' /scratch/stefan/7921153/working/building/REAL250005042153 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042153 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042153/0 /scratch/stefan/7921153/working/building/REAL250005042153 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 262) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/262 `/scratch/stefan/7921153/working/3D/262' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)C(=O)NC[C@@H](C)N(CC)C(=O)C1=CC(=O)[N-]O1) `REAL250005042153.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042153/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042153 none CCC(C)C(=O)NC[C@@H](C)N(CC)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 8, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 191, 111, 191, 111, 111, 64, 35, 19, 35, 35, 7, 19, 26, 1, 7, 1, 1, 1, 1, 1, 1, 194, 194, 194, 194, 194, 191, 191, 191, 191, 111, 64, 64, 35, 35, 35, 26, 26, 26, 26, 26, 1] 201 rigid atoms, others: [42, 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, 41]) total number of confs: 859 number of broken/clashed sets: 116 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042153 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042153 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042153/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042153 Building REAL250005042154 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042154' /scratch/stefan/7921153/working/building/REAL250005042154 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042154 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042154/0 /scratch/stefan/7921153/working/building/REAL250005042154 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 263) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/263 `/scratch/stefan/7921153/working/3D/263' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C1=CC(=O)[N-]O1)[C@H](C)CNC(=O)C(C)OC) `REAL250005042154.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042154.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042154/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042154 none CCN(C(=O)C1=CC(=O)[N-]O1)[C@H](C)CNC(=O)C(C)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 8, 1, 11, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [17, 14, 6, 1, 6, 1, 1, 1, 1, 1, 1, 14, 15, 15, 15, 22, 33, 33, 33, 57, 57, 57, 17, 17, 17, 17, 17, 1, 15, 15, 15, 22, 22, 33, 57, 57, 57, 57, 57, 57, 57] 59 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 27] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 263 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042154 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042154 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042154/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042154 Building REAL250005042155 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042155' /scratch/stefan/7921153/working/building/REAL250005042155 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042155 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042155/0 /scratch/stefan/7921153/working/building/REAL250005042155 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 264) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/264 `/scratch/stefan/7921153/working/3D/264' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCCC(=O)NC[C@@H](C)N(CC)C(=O)C1=CC(=O)[N-]O1) `REAL250005042155.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042155.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042155/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042155 none C=CCCC(=O)NC[C@@H](C)N(CC)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 5, 8, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [57, 57, 55, 20, 20, 20, 16, 13, 13, 13, 13, 6, 13, 14, 1, 6, 1, 1, 1, 1, 1, 1, 57, 57, 57, 57, 57, 55, 55, 20, 16, 16, 13, 13, 13, 14, 14, 14, 14, 14, 1] 61 rigid atoms, others: [40, 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]) total number of confs: 234 number of broken/clashed sets: 60 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042155 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042155 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042155/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042155 Building REAL250005042156 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042156' /scratch/stefan/7921153/working/building/REAL250005042156 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042156 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042156/0 /scratch/stefan/7921153/working/building/REAL250005042156 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 265) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/265 `/scratch/stefan/7921153/working/3D/265' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=C(C)C(=O)NC[C@@H](C)N(CC)C(=O)C1=CC(=O)[N-]O1) `REAL250005042156.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042156.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042156/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042156 none CC=C(C)C(=O)NC[C@@H](C)N(CC)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 7, 5, 8, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 120, 200, 120, 120, 80, 40, 22, 40, 40, 8, 22, 31, 1, 8, 1, 1, 1, 1, 1, 1, 200, 200, 200, 200, 200, 200, 200, 120, 80, 80, 40, 40, 40, 31, 31, 31, 31, 31, 1] 201 rigid atoms, others: [40, 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]) total number of confs: 796 number of broken/clashed sets: 103 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042156 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042156 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042156/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042156 Building REAL250005042157 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042157' /scratch/stefan/7921153/working/building/REAL250005042157 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042157 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042157/0 /scratch/stefan/7921153/working/building/REAL250005042157 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 266) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/266 `/scratch/stefan/7921153/working/3D/266' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C1=CC(=O)[N-]O1)[C@H](C)CNC(=O)C1(C)CC1) `REAL250005042157.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042157.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042157/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042157 none CCN(C(=O)C1=CC(=O)[N-]O1)[C@H](C)CNC(=O)C1(C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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, 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: [86, 60, 48, 60, 83, 83, 132, 132, 132, 132, 132, 30, 48, 48, 7, 7, 1, 7, 1, 1, 1, 1, 86, 86, 86, 86, 86, 132, 48, 48, 48, 30, 30, 7, 2, 2, 2, 1, 1, 1, 1] 132 rigid atoms, others: [37, 38, 39, 40, 16, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 547 number of broken/clashed sets: 27 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042157 none CCN(C(=O)C1=CC(=O)[N-]O1)[C@H](C)CNC(=O)C1(C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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, 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: [16, 13, 6, 1, 6, 1, 1, 1, 1, 1, 1, 13, 24, 24, 24, 41, 73, 74, 73, 132, 132, 132, 16, 16, 16, 16, 16, 1, 24, 24, 24, 41, 41, 74, 132, 132, 132, 132, 132, 132, 132] 132 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 27] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 508 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042157 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042157 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042157/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042157 Building REAL250005042158 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042158' /scratch/stefan/7921153/working/building/REAL250005042158 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042158 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042158/0 /scratch/stefan/7921153/working/building/REAL250005042158 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 267) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/267 `/scratch/stefan/7921153/working/3D/267' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C1=CC(=O)[N-]O1)[C@H](C)CNC(=O)[C@@H]1C[C@H]1C) `REAL250005042158.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042158/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042158 none CCN(C(=O)C1=CC(=O)[N-]O1)[C@H](C)CNC(=O)[C@@H]1C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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, 7, 7, 7] 0 hydrogens 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, 101, 86, 101, 149, 149, 191, 191, 191, 191, 191, 50, 86, 86, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 129, 129, 129, 129, 129, 191, 86, 86, 86, 50, 50, 13, 1, 1, 2, 2, 2] 201 rigid atoms, others: [36, 37, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40]) total number of confs: 838 number of broken/clashed sets: 115 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042158 none CCN(C(=O)C1=CC(=O)[N-]O1)[C@H](C)CNC(=O)[C@@H]1C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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, 7, 7, 7] 0 hydrogens 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, 21, 8, 1, 8, 1, 1, 1, 1, 1, 1, 21, 35, 35, 35, 68, 99, 99, 99, 191, 191, 191, 191, 191, 31, 31, 31, 31, 31, 1, 35, 35, 35, 68, 68, 99, 191, 191, 191, 191, 191] 201 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 29] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 740 number of broken/clashed sets: 115 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042158 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042158 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042158/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042158 Building REAL250005042159 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042159' /scratch/stefan/7921153/working/building/REAL250005042159 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042159 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042159/0 /scratch/stefan/7921153/working/building/REAL250005042159 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 268) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/268 `/scratch/stefan/7921153/working/3D/268' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C1=CC(=O)[N-]O1)[C@H](C)CNC(=O)[C@H]1C[C@@H]1C) `REAL250005042159.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042159.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042159/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042159 none CCN(C(=O)C1=CC(=O)[N-]O1)[C@H](C)CNC(=O)[C@H]1C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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, 7, 7, 7] 0 hydrogens 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, 106, 85, 106, 153, 153, 192, 192, 192, 192, 192, 46, 85, 85, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 133, 133, 133, 133, 133, 192, 85, 85, 85, 46, 46, 12, 1, 1, 2, 2, 2] 201 rigid atoms, others: [36, 37, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40]) total number of confs: 829 number of broken/clashed sets: 122 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042159 none CCN(C(=O)C1=CC(=O)[N-]O1)[C@H](C)CNC(=O)[C@H]1C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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, 7, 7, 7] 0 hydrogens 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, 21, 8, 1, 8, 1, 1, 1, 1, 1, 1, 21, 37, 37, 37, 69, 103, 103, 103, 192, 192, 192, 192, 192, 31, 31, 31, 31, 31, 1, 37, 37, 37, 69, 69, 103, 192, 192, 192, 192, 192] 201 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 29] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 756 number of broken/clashed sets: 122 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042159 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042159 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042159/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042159 Building REAL250005042160 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042160' /scratch/stefan/7921153/working/building/REAL250005042160 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042160 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042160/0 /scratch/stefan/7921153/working/building/REAL250005042160 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 269) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/269 `/scratch/stefan/7921153/working/3D/269' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C1=CC(=O)[N-]O1)[C@H](C)CNC(=O)C(N)=O) `REAL250005042160.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042160.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042160/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042160 none CCN(C(=O)C1=CC(=O)[N-]O1)[C@H](C)CNC(=O)C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 8, 1, 11, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 4, 7, 6, 7, 4, 6, 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: [29, 20, 8, 1, 8, 1, 1, 1, 1, 1, 1, 20, 45, 45, 45, 73, 133, 133, 133, 139, 139, 29, 29, 29, 29, 29, 1, 45, 45, 45, 73, 73, 133, 139, 139] 145 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 26] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 554 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042160 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042160 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042160/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042160 Building REAL250005042161 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042161' /scratch/stefan/7921153/working/building/REAL250005042161 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042161 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042161/0 /scratch/stefan/7921153/working/building/REAL250005042161 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 270) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/270 `/scratch/stefan/7921153/working/3D/270' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C1=CC(=O)[N-]O1)[C@H](C)CNC(=O)C(C)(C)C) `REAL250005042161.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042161/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042161 none CCN(C(=O)C1=CC(=O)[N-]O1)[C@H](C)CNC(=O)C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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, 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: [16, 14, 8, 1, 8, 1, 1, 1, 1, 1, 1, 14, 25, 25, 25, 39, 59, 59, 59, 60, 60, 60, 16, 16, 16, 16, 16, 1, 25, 25, 25, 39, 39, 59, 60, 60, 60, 60, 60, 60, 60, 60, 60] 60 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 27] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 234 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042161 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042161 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042161/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042161 Building REAL250005042162 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042162' /scratch/stefan/7921153/working/building/REAL250005042162 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042162 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042162/0 /scratch/stefan/7921153/working/building/REAL250005042162 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 271) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/271 `/scratch/stefan/7921153/working/3D/271' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC(=O)NC[C@@H](C)N(CC)C(=O)C1=CC(=O)[N-]O1) `REAL250005042162.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042162.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042162/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042162 none C=CCC(=O)NC[C@@H](C)N(CC)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 7, 5, 8, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [172, 168, 83, 83, 83, 53, 32, 22, 32, 32, 8, 22, 32, 1, 8, 1, 1, 1, 1, 1, 1, 172, 172, 172, 168, 168, 83, 53, 53, 32, 32, 32, 32, 32, 32, 32, 32, 1] 179 rigid atoms, others: [37, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 792 number of broken/clashed sets: 118 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042162 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042162 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042162/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042162 Building REAL250005042163 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042163' /scratch/stefan/7921153/working/building/REAL250005042163 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005042163 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042163/0 /scratch/stefan/7921153/working/building/REAL250005042163 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 272) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/272 `/scratch/stefan/7921153/working/3D/272' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C1=CC(=O)[N-]O1)[C@H](C)CNC(=O)C[NH+](C)C) `REAL250005042163.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042163.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042163/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042163 none CCN(C(=O)C1=CC(=O)[N-]O1)[C@H](C)CNC(=O)C[NH+](C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 8, 1, 11, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 4, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 8, 8, 8, 8, 8, 8, 8, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 8, 8, 8, 8, 8, 8, 8, 8, 8] 8 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 28] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 19 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042163 /scratch/stefan/7921153/working /scratch/stefan/7921153 mkdir: created directory `1' /scratch/stefan/7921153/working/building/REAL250005042163/1 /scratch/stefan/7921153/working/building/REAL250005042163 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 1 (index: 273) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/273 `/scratch/stefan/7921153/working/3D/273' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C1=CC(=O)[N-]O1)[C@H](C)CNC(=O)CN(C)C) `REAL250005042163.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005042163.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042163/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.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: REAL250005042163 none CCN(C(=O)C1=CC(=O)[N-]O1)[C@H](C)CNC(=O)CN(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 8, 1, 11, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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, 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: [18, 15, 7, 1, 7, 1, 1, 1, 1, 1, 1, 15, 16, 16, 16, 24, 45, 45, 45, 88, 99, 99, 18, 18, 18, 18, 18, 1, 16, 16, 16, 24, 24, 45, 88, 88, 99, 99, 99, 99, 99, 99] 100 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 27] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 414 number of broken/clashed sets: 71 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042163 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042163 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 1: /scratch/stefan/7921153/working/building/REAL250005042163/1.* 0: /scratch/stefan/7921153/working/building/REAL250005042163/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042163 Building REAL250005042164 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042164' /scratch/stefan/7921153/working/building/REAL250005042164 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042164 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042164/0 /scratch/stefan/7921153/working/building/REAL250005042164 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 274) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/274 `/scratch/stefan/7921153/working/3D/274' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(O)C(=O)NC[C@@H](C)N(CC)C(=O)C1=CC(=O)[N-]O1) `REAL250005042164.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042164.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042164/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042164 none C=CC(O)C(=O)NC[C@@H](C)N(CC)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 8, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 204 conformations in input total number of sets (complete confs): 204 using faster count positions algorithm for large data unique positions, atoms: [65, 65, 34, 65, 34, 34, 22, 15, 13, 15, 15, 7, 13, 16, 1, 7, 1, 1, 1, 1, 1, 1, 65, 65, 65, 65, 195, 34, 22, 22, 15, 15, 15, 16, 16, 16, 16, 16, 1] 204 rigid atoms, others: [38, 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]) total number of confs: 479 number of broken/clashed sets: 147 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042164 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042164 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042164/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042164 Building REAL250005042165 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042165' /scratch/stefan/7921153/working/building/REAL250005042165 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042165 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042165/0 /scratch/stefan/7921153/working/building/REAL250005042165 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 275) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/275 `/scratch/stefan/7921153/working/3D/275' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C1=CC(=O)[N-]O1)[C@H](C)CNC(=O)C1COC1) `REAL250005042165.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042165.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042165/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042165 none CCN(C(=O)C1=CC(=O)[N-]O1)[C@H](C)CNC(=O)C1COC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 8, 1, 11, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [133, 98, 74, 98, 136, 136, 197, 197, 197, 197, 197, 50, 74, 74, 11, 11, 1, 11, 1, 1, 1, 1, 133, 133, 133, 133, 133, 197, 74, 74, 74, 50, 50, 11, 1, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 38, 16, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 811 number of broken/clashed sets: 37 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042165 none CCN(C(=O)C1=CC(=O)[N-]O1)[C@H](C)CNC(=O)C1COC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 8, 1, 11, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 19, 8, 1, 8, 1, 1, 1, 1, 1, 1, 19, 37, 37, 37, 59, 124, 124, 124, 197, 197, 197, 23, 23, 23, 23, 23, 1, 37, 37, 37, 59, 59, 124, 197, 197, 197, 197, 197] 201 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 27] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 679 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042165 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042165 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042165/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042165 Building REAL250005042166 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042166' /scratch/stefan/7921153/working/building/REAL250005042166 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042166 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042166/0 /scratch/stefan/7921153/working/building/REAL250005042166 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 276) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/276 `/scratch/stefan/7921153/working/3D/276' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C1=CC(=O)[N-]O1)[C@H](C)CNC(=O)[C@@H](C)OC) `REAL250005042166.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042166.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042166/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042166 none CCN(C(=O)C1=CC(=O)[N-]O1)[C@H](C)CNC(=O)[C@@H](C)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [15, 13, 6, 1, 6, 1, 1, 1, 1, 1, 1, 13, 14, 14, 14, 20, 31, 31, 31, 55, 55, 55, 55, 15, 15, 15, 15, 15, 1, 14, 14, 14, 20, 20, 31, 55, 55, 55, 55, 55, 55] 58 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 28] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 249 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042166 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042166 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042166/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042166 Building REAL250005042167 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042167' /scratch/stefan/7921153/working/building/REAL250005042167 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042167 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042167/0 /scratch/stefan/7921153/working/building/REAL250005042167 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 277) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/277 `/scratch/stefan/7921153/working/3D/277' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC=CC(=O)NC[C@@H](C)N(CC)C(=O)C1=CC(=O)[N-]O1) `REAL250005042167.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042167/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042167 none CCC=CC(=O)NC[C@@H](C)N(CC)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 7, 5, 8, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [65, 39, 39, 25, 25, 25, 23, 17, 14, 17, 17, 6, 14, 17, 1, 6, 1, 1, 1, 1, 1, 1, 65, 65, 65, 65, 65, 39, 39, 25, 23, 23, 17, 17, 17, 17, 17, 17, 17, 17, 1] 71 rigid atoms, others: [40, 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]) total number of confs: 331 number of broken/clashed sets: 70 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042167 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042167 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042167/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042167 Building REAL250005042168 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042168' /scratch/stefan/7921153/working/building/REAL250005042168 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types Protomer extracton resulted in 0 protomers Marking REAL250005042168 as failed and skipping /scratch/stefan/7921153/working /scratch/stefan/7921153 `/scratch/stefan/7921153/working/building/REAL250005042168' -> `/scratch/stefan/7921153/failed/REAL250005042168' Building REAL250005042169 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042169' /scratch/stefan/7921153/working/building/REAL250005042169 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042169 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042169/0 /scratch/stefan/7921153/working/building/REAL250005042169 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 278) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/278 `/scratch/stefan/7921153/working/3D/278' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C1=CC(=O)[N-]O1)[C@H](C)CNC(=O)CO) `REAL250005042169.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042169.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042169/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042169 none CCN(C(=O)C1=CC(=O)[N-]O1)[C@H](C)CNC(=O)CO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 345 conformations in input total number of sets (complete confs): 345 using faster count positions algorithm for large data unique positions, atoms: [24, 19, 8, 1, 8, 1, 1, 1, 1, 1, 1, 19, 38, 38, 38, 67, 109, 109, 109, 114, 24, 24, 24, 24, 24, 1, 38, 38, 38, 67, 67, 109, 114, 114, 342] 345 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 25] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 819 number of broken/clashed sets: 75 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042169 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042169 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042169/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042169 Building REAL250005042170 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042170' /scratch/stefan/7921153/working/building/REAL250005042170 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042170 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042170/0 /scratch/stefan/7921153/working/building/REAL250005042170 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 279) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/279 `/scratch/stefan/7921153/working/3D/279' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C1=CC(=O)[N-]O1)[C@H](C)CNC(=O)C(C)O) `REAL250005042170.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042170/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042170 none CCN(C(=O)C1=CC(=O)[N-]O1)[C@H](C)CNC(=O)C(C)O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 8, 1, 11, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 444 conformations in input total number of sets (complete confs): 444 using faster count positions algorithm for large data unique positions, atoms: [27, 21, 8, 1, 8, 1, 1, 1, 1, 1, 1, 21, 39, 39, 39, 71, 132, 133, 132, 148, 147, 27, 27, 27, 27, 27, 1, 39, 39, 39, 71, 71, 133, 148, 148, 148, 148, 444] 444 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 26] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 1050 number of broken/clashed sets: 93 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042170 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042170 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042170/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042170 Building REAL250005042171 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042171' /scratch/stefan/7921153/working/building/REAL250005042171 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042171 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042171/0 /scratch/stefan/7921153/working/building/REAL250005042171 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 280) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/280 `/scratch/stefan/7921153/working/3D/280' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C1=CC(=O)[N-]O1)[C@H](C)CNC(=O)C1CC1F) `REAL250005042171.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042171/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042171 none CCN(C(=O)C1=CC(=O)[N-]O1)[C@H](C)CNC(=O)C1CC1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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] 0 hydrogens 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, 106, 82, 106, 135, 135, 199, 199, 199, 199, 199, 52, 82, 82, 11, 11, 1, 11, 1, 1, 1, 1, 140, 140, 140, 140, 140, 199, 82, 82, 82, 52, 52, 11, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 16, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 825 number of broken/clashed sets: 38 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042171 none CCN(C(=O)C1=CC(=O)[N-]O1)[C@H](C)CNC(=O)C1CC1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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] 0 hydrogens 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, 19, 9, 1, 9, 1, 1, 1, 1, 1, 1, 19, 35, 35, 35, 57, 113, 113, 113, 199, 199, 199, 22, 22, 22, 22, 22, 1, 35, 35, 35, 57, 57, 113, 199, 199, 199, 199] 201 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 27] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 689 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042171 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042171 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042171/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042171 Building REAL250005042172 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042172' /scratch/stefan/7921153/working/building/REAL250005042172 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042172 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042172/0 /scratch/stefan/7921153/working/building/REAL250005042172 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 281) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/281 `/scratch/stefan/7921153/working/3D/281' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C1=CC(=O)[N-]O1)[C@H](C)CNC(=O)CCF) `REAL250005042172.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042172.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042172/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042172 none CCN(C(=O)C1=CC(=O)[N-]O1)[C@H](C)CNC(=O)CCF NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 8, 1, 11, 5, 5, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 13, 8, 1, 8, 1, 1, 1, 1, 1, 1, 13, 21, 21, 21, 39, 85, 85, 85, 196, 196, 16, 16, 16, 16, 16, 1, 21, 21, 21, 39, 39, 85, 196, 196, 196, 196] 201 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 26] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 802 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042172 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042172 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042172/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042172 Building REAL250005042173 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042173' /scratch/stefan/7921153/working/building/REAL250005042173 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042173 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042173/0 /scratch/stefan/7921153/working/building/REAL250005042173 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 282) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/282 `/scratch/stefan/7921153/working/3D/282' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C1=CC(=O)[N-]O1)[C@H](C)CNC(=O)C=CCF) `REAL250005042173.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042173/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042173 none CCN(C(=O)C1=CC(=O)[N-]O1)[C@H](C)CNC(=O)C=CCF NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 8, 1, 11, 1, 1, 5, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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] 0 hydrogens 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, 20, 8, 1, 8, 1, 1, 1, 1, 1, 1, 20, 33, 33, 33, 65, 99, 99, 99, 172, 172, 193, 28, 28, 28, 28, 28, 1, 33, 33, 33, 65, 65, 99, 172, 172, 193, 193] 201 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 27] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 805 number of broken/clashed sets: 116 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042173 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042173 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042173/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042173 Building REAL250005042174 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042174' /scratch/stefan/7921153/working/building/REAL250005042174 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042174 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042174/0 /scratch/stefan/7921153/working/building/REAL250005042174 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 283) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/283 `/scratch/stefan/7921153/working/3D/283' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCC(=O)NC[C@@H](C)N(CC)C(=O)C1=CC(=O)[N-]O1) `REAL250005042174.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042174/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042174 none C#CCCC(=O)NC[C@@H](C)N(CC)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 5, 8, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [40, 40, 40, 26, 26, 26, 17, 15, 12, 15, 15, 6, 12, 16, 1, 6, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 40, 26, 17, 17, 15, 15, 15, 16, 16, 16, 16, 16, 1] 45 rigid atoms, others: [38, 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]) total number of confs: 178 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042174 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042174 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042174/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042174 Building REAL250005042175 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042175' /scratch/stefan/7921153/working/building/REAL250005042175 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042175 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042175/0 /scratch/stefan/7921153/working/building/REAL250005042175 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 284) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/284 `/scratch/stefan/7921153/working/3D/284' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C1=CC(=O)[N-]O1)[C@H](C)CNC(=O)C1CCO1) `REAL250005042175.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042175/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042175 none CCN(C(=O)C1=CC(=O)[N-]O1)[C@H](C)CNC(=O)C1CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [68, 62, 58, 62, 71, 71, 76, 76, 76, 76, 76, 42, 58, 58, 11, 11, 1, 11, 1, 1, 1, 1, 68, 68, 68, 68, 68, 76, 58, 58, 58, 42, 42, 11, 1, 1, 1, 1, 1] 79 rigid atoms, others: [34, 35, 36, 37, 38, 16, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 334 number of broken/clashed sets: 50 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042175 none CCN(C(=O)C1=CC(=O)[N-]O1)[C@H](C)CNC(=O)C1CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [21, 18, 7, 1, 7, 1, 1, 1, 1, 1, 1, 18, 19, 19, 19, 28, 43, 43, 43, 76, 76, 76, 21, 21, 21, 21, 21, 1, 19, 19, 19, 28, 28, 43, 76, 76, 76, 76, 76] 79 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 27] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 276 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042175 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042175 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042175/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042175 Building REAL250005042176 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042176' /scratch/stefan/7921153/working/building/REAL250005042176 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042176 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042176/0 /scratch/stefan/7921153/working/building/REAL250005042176 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 285) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/285 `/scratch/stefan/7921153/working/3D/285' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C1=CC(=O)[N-]O1)[C@H](C)CNC(=O)C(C)(C)O) `REAL250005042176.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042176/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042176 none CCN(C(=O)C1=CC(=O)[N-]O1)[C@H](C)CNC(=O)C(C)(C)O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 480 conformations in input total number of sets (complete confs): 480 using faster count positions algorithm for large data unique positions, atoms: [25, 19, 9, 1, 9, 1, 1, 1, 1, 1, 1, 19, 35, 35, 35, 60, 126, 126, 126, 160, 160, 158, 25, 25, 25, 25, 25, 1, 35, 35, 35, 60, 60, 126, 160, 160, 160, 160, 160, 160, 480] 480 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 27] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 1132 number of broken/clashed sets: 96 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042176 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042176 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042176/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042176 Building REAL250005042177 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042177' /scratch/stefan/7921153/working/building/REAL250005042177 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042177 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042177/0 /scratch/stefan/7921153/working/building/REAL250005042177 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 286) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/286 `/scratch/stefan/7921153/working/3D/286' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C1=CC(=O)[N-]O1)[C@H](C)CNC(=O)C1C=C1C) `REAL250005042177.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042177.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042177/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042177 none CCN(C(=O)C1=CC(=O)[N-]O1)[C@H](C)CNC(=O)C1C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 8, 1, 11, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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, 7] 0 hydrogens 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, 118, 105, 118, 156, 156, 195, 195, 195, 195, 195, 60, 105, 105, 13, 13, 1, 13, 1, 1, 1, 1, 147, 147, 147, 147, 147, 195, 105, 105, 105, 60, 60, 13, 1, 1, 2, 2, 2] 201 rigid atoms, others: [34, 35, 16, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38]) total number of confs: 885 number of broken/clashed sets: 110 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042177 none CCN(C(=O)C1=CC(=O)[N-]O1)[C@H](C)CNC(=O)C1C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 8, 1, 11, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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, 7] 0 hydrogens 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, 22, 8, 1, 8, 1, 1, 1, 1, 1, 1, 22, 35, 35, 35, 64, 93, 93, 93, 195, 195, 195, 31, 31, 31, 31, 31, 1, 35, 35, 35, 64, 64, 93, 195, 195, 195, 195, 195] 201 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 27] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 724 number of broken/clashed sets: 110 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042177 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042177 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042177/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042177 Building REAL250005042178 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042178' /scratch/stefan/7921153/working/building/REAL250005042178 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042178 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042178/0 /scratch/stefan/7921153/working/building/REAL250005042178 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 287) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/287 `/scratch/stefan/7921153/working/3D/287' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C1=CC(=O)[N-]O1)[C@H](C)CNC(=O)[C@@H](C)O) `REAL250005042178.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042178.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042178/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042178 none CCN(C(=O)C1=CC(=O)[N-]O1)[C@H](C)CNC(=O)[C@@H](C)O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 378 conformations in input total number of sets (complete confs): 378 using faster count positions algorithm for large data unique positions, atoms: [24, 18, 8, 1, 8, 1, 1, 1, 1, 1, 1, 18, 33, 33, 33, 62, 112, 113, 113, 126, 126, 126, 24, 24, 24, 24, 24, 1, 33, 33, 33, 62, 62, 113, 126, 126, 126, 378] 378 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 27] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 900 number of broken/clashed sets: 57 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042178 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042178 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042178/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042178 Building REAL250005042179 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042179' /scratch/stefan/7921153/working/building/REAL250005042179 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042179 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042179/0 /scratch/stefan/7921153/working/building/REAL250005042179 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 288) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/288 `/scratch/stefan/7921153/working/3D/288' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C1=CC(=O)[N-]O1)[C@H](C)CNC(=O)C=CCO) `REAL250005042179.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042179.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042179/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042179 none CCN(C(=O)C1=CC(=O)[N-]O1)[C@H](C)CNC(=O)C=CCO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 8, 1, 11, 1, 1, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [27, 19, 8, 1, 8, 1, 1, 1, 1, 1, 1, 19, 30, 30, 30, 59, 91, 91, 91, 168, 168, 193, 27, 27, 27, 27, 27, 1, 30, 30, 30, 59, 59, 91, 168, 168, 193, 193, 579] 603 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 27] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 1385 number of broken/clashed sets: 324 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042179 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042179 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042179/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042179 Building REAL250005042180 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042180' /scratch/stefan/7921153/working/building/REAL250005042180 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042180 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042180/0 /scratch/stefan/7921153/working/building/REAL250005042180 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 289) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/289 `/scratch/stefan/7921153/working/3D/289' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C1=CC(=O)[N-]O1)[C@H](C)CNC(=O)C1=CCC1) `REAL250005042180.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042180.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042180/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042180 none CCN(C(=O)C1=CC(=O)[N-]O1)[C@H](C)CNC(=O)C1=CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 8, 1, 11, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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, 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: [80, 64, 46, 64, 84, 84, 112, 112, 112, 112, 112, 25, 46, 45, 8, 8, 1, 8, 1, 1, 1, 1, 80, 80, 80, 80, 80, 112, 46, 46, 46, 25, 25, 8, 1, 1, 1, 1, 1] 118 rigid atoms, others: [34, 35, 36, 37, 38, 16, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 464 number of broken/clashed sets: 71 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042180 none CCN(C(=O)C1=CC(=O)[N-]O1)[C@H](C)CNC(=O)C1=CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 8, 1, 11, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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, 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: [33, 25, 8, 1, 8, 1, 1, 1, 1, 1, 1, 25, 47, 47, 47, 90, 112, 112, 112, 112, 112, 112, 33, 33, 33, 33, 33, 1, 47, 47, 47, 90, 90, 112, 112, 112, 112, 112, 112] 118 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 27] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 491 number of broken/clashed sets: 71 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042180 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042180 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042180/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042180 Building REAL250005042181 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042181' /scratch/stefan/7921153/working/building/REAL250005042181 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042181 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042181/0 /scratch/stefan/7921153/working/building/REAL250005042181 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 290) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/290 `/scratch/stefan/7921153/working/3D/290' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C1=CC(=O)[N-]O1)[C@H](C)CNC(=O)C=NOC) `REAL250005042181.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042181.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042181/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042181 none CCN(C(=O)C1=CC(=O)[N-]O1)[C@H](C)CNC(=O)C=NOC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 8, 1, 11, 1, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 113 conformations in input total number of sets (complete confs): 113 using faster count positions algorithm for large data unique positions, atoms: [24, 19, 8, 1, 8, 1, 1, 1, 1, 1, 1, 19, 21, 21, 21, 33, 59, 59, 59, 108, 108, 108, 24, 24, 24, 24, 24, 1, 21, 21, 21, 33, 33, 59, 108, 108, 108, 108] 113 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 27] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 386 number of broken/clashed sets: 86 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042181 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042181 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042181/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042181 Building REAL250005042182 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042182' /scratch/stefan/7921153/working/building/REAL250005042182 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042182 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042182/0 /scratch/stefan/7921153/working/building/REAL250005042182 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 291) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/291 `/scratch/stefan/7921153/working/3D/291' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C1=CC(=O)[N-]O1)[C@H](C)CNC(=O)C1(F)CC1) `REAL250005042182.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042182.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042182/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042182 none CCN(C(=O)C1=CC(=O)[N-]O1)[C@H](C)CNC(=O)C1(F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 8, 1, 11, 5, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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] 0 hydrogens 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, 99, 75, 99, 136, 136, 197, 197, 197, 197, 197, 51, 75, 75, 10, 10, 1, 10, 1, 1, 1, 1, 143, 143, 143, 143, 143, 197, 75, 75, 75, 51, 51, 10, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 16, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 889 number of broken/clashed sets: 33 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042182 none CCN(C(=O)C1=CC(=O)[N-]O1)[C@H](C)CNC(=O)C1(F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 8, 1, 11, 5, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 21, 9, 1, 9, 1, 1, 1, 1, 1, 1, 21, 37, 37, 37, 62, 134, 134, 134, 197, 197, 197, 27, 27, 27, 27, 27, 1, 37, 37, 37, 62, 62, 134, 197, 197, 197, 197] 201 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 27] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 702 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042182 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042182 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042182/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042182 Building REAL250005042183 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042183' /scratch/stefan/7921153/working/building/REAL250005042183 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042183 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042183/0 /scratch/stefan/7921153/working/building/REAL250005042183 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 292) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/292 `/scratch/stefan/7921153/working/3D/292' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=C(F)C(=O)NC[C@@H](C)N(CC)C(=O)C1=CC(=O)[N-]O1) `REAL250005042183.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042183/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042183 none CC=C(F)C(=O)NC[C@@H](C)N(CC)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 15, 1, 11, 8, 5, 5, 7, 5, 8, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [197, 197, 172, 197, 172, 172, 108, 54, 29, 54, 54, 10, 29, 40, 1, 10, 1, 1, 1, 1, 1, 1, 197, 197, 197, 197, 172, 108, 108, 54, 54, 54, 40, 40, 40, 40, 40, 1] 201 rigid atoms, others: [37, 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]) total number of confs: 815 number of broken/clashed sets: 90 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042183 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042183 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042183/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042183 Building REAL250005042184 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042184' /scratch/stefan/7921153/working/building/REAL250005042184 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042184 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042184/0 /scratch/stefan/7921153/working/building/REAL250005042184 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 293) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/293 `/scratch/stefan/7921153/working/3D/293' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C1=CC(=O)[N-]O1)[C@H](C)CNC(=O)C(C)CO) `REAL250005042184.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042184.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042184/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042184 none CCN(C(=O)C1=CC(=O)[N-]O1)[C@H](C)CNC(=O)C(C)CO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [28, 20, 8, 1, 8, 1, 1, 1, 1, 1, 1, 20, 34, 34, 34, 64, 104, 104, 104, 189, 189, 190, 28, 28, 28, 28, 28, 1, 34, 34, 34, 64, 64, 104, 189, 189, 189, 189, 190, 190, 570] 603 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 27] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 1419 number of broken/clashed sets: 353 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042184 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042184 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042184/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042184 Building REAL250005042185 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042185' /scratch/stefan/7921153/working/building/REAL250005042185 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042185 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042185/0 /scratch/stefan/7921153/working/building/REAL250005042185 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 294) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/294 `/scratch/stefan/7921153/working/3D/294' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C1=CC(=O)[N-]O1)[C@H](C)CNC(=O)[C@H](C)O) `REAL250005042185.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042185.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042185/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042185 none CCN(C(=O)C1=CC(=O)[N-]O1)[C@H](C)CNC(=O)[C@H](C)O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 453 conformations in input total number of sets (complete confs): 453 using faster count positions algorithm for large data unique positions, atoms: [27, 22, 8, 1, 8, 1, 1, 1, 1, 1, 1, 22, 40, 40, 40, 73, 135, 136, 135, 151, 151, 150, 27, 27, 27, 27, 27, 1, 40, 40, 40, 73, 73, 136, 151, 151, 151, 453] 453 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 27] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 1067 number of broken/clashed sets: 96 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042185 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042185 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042185/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042185 Building REAL250005042186 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042186' /scratch/stefan/7921153/working/building/REAL250005042186 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042186 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042186/0 /scratch/stefan/7921153/working/building/REAL250005042186 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 295) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/295 `/scratch/stefan/7921153/working/3D/295' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C1CC1C(=O)NC[C@@H](C)N(CC)C(=O)C1=CC(=O)[N-]O1) `REAL250005042186.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042186.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042186/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042186 none C=C1CC1C(=O)NC[C@@H](C)N(CC)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 5, 8, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 105, 105, 105, 73, 39, 22, 39, 39, 8, 22, 30, 1, 8, 1, 1, 1, 1, 1, 1, 200, 200, 200, 200, 200, 105, 73, 73, 39, 39, 39, 30, 30, 30, 30, 30, 1] 201 rigid atoms, others: [38, 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]) total number of confs: 744 number of broken/clashed sets: 99 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042186 none C=C1CC1C(=O)NC[C@@H](C)N(CC)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 5, 8, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 12, 12, 12, 56, 97, 97, 97, 117, 139, 117, 154, 154, 200, 200, 200, 200, 200, 1, 1, 1, 1, 1, 12, 56, 56, 97, 97, 97, 139, 139, 139, 139, 139, 200] 201 rigid atoms, others: [0, 1, 2, 3, 4, 22, 23, 24, 25, 26] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 813 number of broken/clashed sets: 99 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042186 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042186 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042186/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042186 Building REAL250005042187 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042187' /scratch/stefan/7921153/working/building/REAL250005042187 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042187 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042187/0 /scratch/stefan/7921153/working/building/REAL250005042187 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 296) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/296 `/scratch/stefan/7921153/working/3D/296' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C(C)CC(=O)NC[C@@H](C)N(CC)C(=O)C1=CC(=O)[N-]O1) `REAL250005042187.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042187.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042187/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042187 none C=C(C)CC(=O)NC[C@@H](C)N(CC)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 5, 8, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 188, 192, 83, 83, 83, 50, 28, 18, 28, 28, 7, 18, 24, 1, 7, 1, 1, 1, 1, 1, 1, 192, 192, 192, 192, 192, 188, 188, 83, 50, 50, 28, 28, 28, 24, 24, 24, 24, 24, 1] 201 rigid atoms, others: [40, 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]) total number of confs: 839 number of broken/clashed sets: 128 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042187 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042187 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042187/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042187 Building REAL250005042188 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042188' /scratch/stefan/7921153/working/building/REAL250005042188 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042188 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042188/0 /scratch/stefan/7921153/working/building/REAL250005042188 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 297) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/297 `/scratch/stefan/7921153/working/3D/297' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=CC(=O)NC[C@@H](C)N(CC)C(=O)C1=CC(=O)[N-]O1) `REAL250005042188.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042188.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042188/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042188 none CC=CC(=O)NC[C@@H](C)N(CC)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 7, 5, 8, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 140, 140, 140, 95, 50, 26, 50, 50, 10, 26, 34, 1, 10, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 140, 95, 95, 50, 50, 50, 34, 34, 34, 34, 34, 1] 201 rigid atoms, others: [37, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 831 number of broken/clashed sets: 112 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042188 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042188 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042188/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042188 Building REAL250005042189 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042189' /scratch/stefan/7921153/working/building/REAL250005042189 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042189 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042189/0 /scratch/stefan/7921153/working/building/REAL250005042189 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 298) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/298 `/scratch/stefan/7921153/working/3D/298' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C1=CC(=O)[N-]O1)[C@H](C)CNC(=O)[C@@H]1C[C@H]1C) `REAL250005042189.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042189.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042189/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042189 none CCN(C(=O)C1=CC(=O)[N-]O1)[C@H](C)CNC(=O)[C@@H]1C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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, 7, 7, 7] 0 hydrogens 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, 101, 86, 101, 149, 149, 191, 191, 191, 191, 191, 50, 86, 86, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 129, 129, 129, 129, 129, 191, 86, 86, 86, 50, 50, 13, 1, 1, 2, 2, 2] 201 rigid atoms, others: [36, 37, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40]) total number of confs: 838 number of broken/clashed sets: 115 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042189 none CCN(C(=O)C1=CC(=O)[N-]O1)[C@H](C)CNC(=O)[C@@H]1C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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, 7, 7, 7] 0 hydrogens 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, 21, 8, 1, 8, 1, 1, 1, 1, 1, 1, 21, 35, 35, 35, 68, 99, 99, 99, 191, 191, 191, 191, 191, 31, 31, 31, 31, 31, 1, 35, 35, 35, 68, 68, 99, 191, 191, 191, 191, 191] 201 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 29] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 740 number of broken/clashed sets: 115 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042189 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042189 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042189/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042189 Building REAL250005042190 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042190' /scratch/stefan/7921153/working/building/REAL250005042190 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042190 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042190/0 /scratch/stefan/7921153/working/building/REAL250005042190 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 299) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/299 `/scratch/stefan/7921153/working/3D/299' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C1=CC(=O)[N-]O1)[C@H](C)CNC(=O)C1(O)CC1) `REAL250005042190.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042190/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042190 none CCN(C(=O)C1=CC(=O)[N-]O1)[C@H](C)CNC(=O)C1(O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 525 conformations in input total number of sets (complete confs): 525 using faster count positions algorithm for large data unique positions, atoms: [121, 86, 69, 86, 116, 116, 169, 169, 169, 169, 169, 49, 69, 69, 9, 9, 1, 9, 1, 1, 1, 1, 121, 121, 121, 121, 121, 169, 69, 69, 69, 49, 49, 9, 6, 1, 1, 1, 1] 525 rigid atoms, others: [35, 36, 37, 38, 16, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 742 number of broken/clashed sets: 96 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042190 none CCN(C(=O)C1=CC(=O)[N-]O1)[C@H](C)CNC(=O)C1(O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 525 conformations in input total number of sets (complete confs): 525 using faster count positions algorithm for large data unique positions, atoms: [24, 19, 8, 1, 8, 1, 1, 1, 1, 1, 1, 19, 36, 36, 36, 60, 129, 129, 129, 169, 169, 169, 24, 24, 24, 24, 24, 1, 36, 36, 36, 60, 60, 129, 507, 169, 169, 169, 169] 525 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 27] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 1118 number of broken/clashed sets: 96 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042190 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042190 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042190/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042190 Building REAL250005042191 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042191' /scratch/stefan/7921153/working/building/REAL250005042191 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042191 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042191/0 /scratch/stefan/7921153/working/building/REAL250005042191 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 300) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/300 `/scratch/stefan/7921153/working/3D/300' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)CC1CC1)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005042191.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042191/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042191 none CCN(C(=O)CC1CC1)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [115, 87, 49, 87, 111, 111, 136, 172, 172, 18, 49, 48, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 115, 115, 115, 115, 115, 136, 136, 172, 172, 172, 172, 172, 49, 49, 49, 18, 18, 4, 1] 201 rigid atoms, others: [40, 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]) total number of confs: 851 number of broken/clashed sets: 94 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042191 none CCN(C(=O)CC1CC1)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 38, 13, 3, 13, 1, 1, 1, 1, 38, 55, 55, 55, 108, 172, 172, 172, 172, 172, 172, 172, 172, 50, 50, 50, 50, 50, 3, 3, 1, 1, 1, 1, 1, 55, 55, 55, 108, 108, 172, 172] 201 rigid atoms, others: [32, 33, 5, 6, 7, 8, 29, 30, 31] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 701 number of broken/clashed sets: 94 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042191 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042191 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042191/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042191 Building REAL250005042192 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042192' /scratch/stefan/7921153/working/building/REAL250005042192 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042192 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042192/0 /scratch/stefan/7921153/working/building/REAL250005042192 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 301) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/301 `/scratch/stefan/7921153/working/3D/301' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)COC)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005042192.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042192/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042192 none CCN(C(=O)COC)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 84, 47, 84, 107, 107, 168, 179, 19, 47, 46, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 109, 109, 109, 109, 109, 168, 168, 179, 179, 179, 47, 47, 47, 19, 19, 4, 1] 201 rigid atoms, others: [37, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 876 number of broken/clashed sets: 101 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042192 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042192 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042192/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042192 Building REAL250005042193 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042193' /scratch/stefan/7921153/working/building/REAL250005042193 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042193 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042193/0 /scratch/stefan/7921153/working/building/REAL250005042193 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 302) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/302 `/scratch/stefan/7921153/working/3D/302' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(=O)N(CC)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005042193.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042193.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042193/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042193 none CCCC(=O)N(CC)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 172, 112, 88, 112, 49, 88, 115, 21, 49, 46, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 178, 178, 178, 178, 178, 172, 172, 115, 115, 115, 115, 115, 49, 49, 49, 21, 21, 7, 1] 201 rigid atoms, others: [39, 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]) total number of confs: 912 number of broken/clashed sets: 86 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042193 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042193 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042193/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042193 Building REAL250005042194 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042194' /scratch/stefan/7921153/working/building/REAL250005042194 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042194 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042194/0 /scratch/stefan/7921153/working/building/REAL250005042194 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 303) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/303 `/scratch/stefan/7921153/working/3D/303' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)CC(C)C)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005042194.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042194/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042194 none CCN(C(=O)CC(C)C)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [121, 92, 55, 92, 126, 126, 167, 167, 167, 21, 55, 52, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 121, 121, 121, 121, 121, 167, 167, 167, 167, 167, 167, 167, 167, 167, 55, 55, 55, 21, 21, 7, 1] 193 rigid atoms, others: [42, 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, 41]) total number of confs: 873 number of broken/clashed sets: 132 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042194 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042194 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042194/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042194 Building REAL250005042195 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042195' /scratch/stefan/7921153/working/building/REAL250005042195 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042195 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042195/0 /scratch/stefan/7921153/working/building/REAL250005042195 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 304) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/304 `/scratch/stefan/7921153/working/3D/304' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C1CC1C)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005042195.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042195.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042195/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042195 none CCN(C(=O)C1CC1C)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [109, 82, 54, 82, 99, 99, 129, 129, 129, 24, 54, 53, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 109, 109, 109, 109, 109, 129, 129, 129, 129, 129, 129, 129, 54, 54, 54, 24, 24, 9, 1] 161 rigid atoms, others: [40, 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]) total number of confs: 647 number of broken/clashed sets: 64 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042195 none CCN(C(=O)C1CC1C)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [28, 18, 8, 1, 8, 1, 1, 1, 1, 18, 37, 37, 37, 76, 125, 125, 125, 129, 129, 129, 129, 129, 28, 28, 28, 28, 28, 1, 1, 1, 1, 2, 2, 2, 37, 37, 37, 76, 76, 125, 129] 161 rigid atoms, others: [3, 5, 6, 7, 8, 27, 28, 29, 30] set([0, 1, 2, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 545 number of broken/clashed sets: 64 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042195 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042195 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042195/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042195 Building REAL250005042196 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042196' /scratch/stefan/7921153/working/building/REAL250005042196 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042196 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042196/0 /scratch/stefan/7921153/working/building/REAL250005042196 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 305) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/305 `/scratch/stefan/7921153/working/3D/305' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCC(=O)N(CC)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005042196.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042196.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042196/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042196 none CCOCC(=O)N(CC)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 126, 79, 61, 79, 35, 61, 88, 14, 35, 34, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 158, 158, 158, 158, 158, 126, 126, 88, 88, 88, 88, 88, 35, 35, 35, 14, 14, 4, 1] 201 rigid atoms, others: [40, 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]) total number of confs: 756 number of broken/clashed sets: 79 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042196 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042196 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042196/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042196 Building REAL250005042197 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042197' /scratch/stefan/7921153/working/building/REAL250005042197 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042197 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042197/0 /scratch/stefan/7921153/working/building/REAL250005042197 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 306) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/306 `/scratch/stefan/7921153/working/3D/306' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C=C(C)C)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005042197.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042197.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042197/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042197 none CCN(C(=O)C=C(C)C)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [118, 93, 57, 93, 106, 106, 165, 165, 165, 27, 57, 55, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 118, 118, 118, 118, 118, 165, 165, 165, 165, 165, 165, 165, 57, 57, 57, 27, 27, 9, 1] 196 rigid atoms, others: [40, 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]) total number of confs: 755 number of broken/clashed sets: 91 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042197 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042197 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042197/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042197 Building REAL250005042198 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042198' /scratch/stefan/7921153/working/building/REAL250005042198 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042198 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042198/0 /scratch/stefan/7921153/working/building/REAL250005042198 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 307) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/307 `/scratch/stefan/7921153/working/3D/307' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCC(=O)N(CC)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005042198.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042198.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042198/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042198 none CCCCC(=O)N(CC)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 155, 142, 93, 69, 93, 44, 69, 96, 14, 44, 42, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 172, 172, 172, 172, 172, 161, 161, 142, 142, 96, 96, 96, 96, 96, 44, 44, 44, 14, 14, 4, 1] 201 rigid atoms, others: [42, 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, 41]) total number of confs: 946 number of broken/clashed sets: 74 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042198 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042198 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042198/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042198 Building REAL250005042199 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042199' /scratch/stefan/7921153/working/building/REAL250005042199 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042199 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042199/0 /scratch/stefan/7921153/working/building/REAL250005042199 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 308) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/308 `/scratch/stefan/7921153/working/3D/308' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C(C)C)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005042199.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042199.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042199/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042199 none CCN(C(=O)C(C)C)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [100, 77, 49, 77, 105, 105, 120, 120, 22, 49, 47, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 100, 100, 100, 100, 100, 120, 120, 120, 120, 120, 120, 120, 49, 49, 49, 22, 22, 8, 1] 128 rigid atoms, others: [39, 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]) total number of confs: 605 number of broken/clashed sets: 62 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042199 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042199 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042199/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042199 Building REAL250005042200 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042200' /scratch/stefan/7921153/working/building/REAL250005042200 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042200 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042200/0 /scratch/stefan/7921153/working/building/REAL250005042200 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 309) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/309 `/scratch/stefan/7921153/working/3D/309' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)C(=O)N(CC)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005042200.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042200.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042200/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042200 none CCC(C)C(=O)N(CC)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [151, 137, 107, 137, 84, 107, 45, 84, 112, 16, 45, 42, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 152, 152, 152, 152, 152, 137, 137, 137, 137, 112, 112, 112, 112, 112, 45, 45, 45, 16, 16, 4, 1] 167 rigid atoms, others: [42, 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, 41]) total number of confs: 815 number of broken/clashed sets: 101 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042200 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042200 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042200/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042200 Building REAL250005042201 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042201' /scratch/stefan/7921153/working/building/REAL250005042201 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042201 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042201/0 /scratch/stefan/7921153/working/building/REAL250005042201 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 310) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/310 `/scratch/stefan/7921153/working/3D/310' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C(C)OC)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005042201.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042201/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042201 none CCN(C(=O)C(C)OC)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [80, 64, 41, 64, 78, 78, 93, 93, 99, 17, 41, 41, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 80, 80, 80, 80, 80, 93, 93, 93, 93, 99, 99, 99, 41, 41, 41, 17, 17, 4, 1] 107 rigid atoms, others: [40, 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]) total number of confs: 490 number of broken/clashed sets: 67 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042201 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042201 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042201/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042201 Building REAL250005042202 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042202' /scratch/stefan/7921153/working/building/REAL250005042202 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042202 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042202/0 /scratch/stefan/7921153/working/building/REAL250005042202 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 311) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/311 `/scratch/stefan/7921153/working/3D/311' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCCC(=O)N(CC)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005042202.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042202/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042202 none C=CCCC(=O)N(CC)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 172, 170, 123, 96, 123, 52, 96, 131, 20, 52, 49, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 180, 180, 180, 172, 172, 170, 170, 131, 131, 131, 131, 131, 52, 52, 52, 20, 20, 4, 1] 201 rigid atoms, others: [40, 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]) total number of confs: 949 number of broken/clashed sets: 87 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042202 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042202 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042202/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042202 Building REAL250005042203 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042203' /scratch/stefan/7921153/working/building/REAL250005042203 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042203 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042203/0 /scratch/stefan/7921153/working/building/REAL250005042203 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 312) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/312 `/scratch/stefan/7921153/working/3D/312' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C(C)C#N)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005042203.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042203.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042203/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042203 none CCN(C(=O)C(C)C#N)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.1', 'N.1', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 1, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 181 conformations in input total number of sets (complete confs): 181 using faster count positions algorithm for large data unique positions, atoms: [131, 102, 66, 102, 137, 137, 160, 160, 160, 25, 66, 62, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 131, 131, 131, 131, 131, 160, 160, 160, 160, 66, 66, 66, 25, 25, 8, 1] 181 rigid atoms, others: [37, 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]) total number of confs: 813 number of broken/clashed sets: 120 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042203 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042203 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042203/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042203 Building REAL250005042204 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042204' /scratch/stefan/7921153/working/building/REAL250005042204 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042204 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042204/0 /scratch/stefan/7921153/working/building/REAL250005042204 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 313) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/313 `/scratch/stefan/7921153/working/3D/313' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=C(C)C(=O)N(CC)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005042204.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042204/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042204 none CC=C(C)C(=O)N(CC)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 112, 175, 91, 112, 57, 91, 115, 27, 57, 55, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 175, 175, 175, 175, 175, 175, 175, 115, 115, 115, 115, 115, 57, 57, 57, 27, 27, 9, 1] 201 rigid atoms, others: [40, 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]) total number of confs: 806 number of broken/clashed sets: 90 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042204 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042204 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042204/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042204 Building REAL250005042205 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042205' /scratch/stefan/7921153/working/building/REAL250005042205 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042205 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042205/0 /scratch/stefan/7921153/working/building/REAL250005042205 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 314) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/314 `/scratch/stefan/7921153/working/3D/314' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N(CC)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005042205.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042205.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042205/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042205 none CCC(=O)N(CC)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [126, 112, 94, 112, 56, 94, 124, 23, 56, 53, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 126, 126, 126, 126, 126, 124, 124, 124, 124, 124, 56, 56, 56, 23, 23, 8, 1] 143 rigid atoms, others: [36, 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]) total number of confs: 678 number of broken/clashed sets: 70 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042205 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042205 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042205/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042205 Building REAL250005042206 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042206' /scratch/stefan/7921153/working/building/REAL250005042206 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042206 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042206/0 /scratch/stefan/7921153/working/building/REAL250005042206 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 315) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/315 `/scratch/stefan/7921153/working/3D/315' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)CCOC)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005042206.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042206/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042206 none CCN(C(=O)CCOC)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 92, 55, 92, 125, 125, 162, 167, 172, 20, 55, 53, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 124, 124, 124, 124, 124, 162, 162, 167, 167, 172, 172, 172, 55, 55, 55, 20, 20, 5, 1] 201 rigid atoms, others: [40, 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]) total number of confs: 869 number of broken/clashed sets: 80 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042206 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042206 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042206/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042206 Building REAL250005042207 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042207' /scratch/stefan/7921153/working/building/REAL250005042207 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042207 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042207/0 /scratch/stefan/7921153/working/building/REAL250005042207 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 316) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/316 `/scratch/stefan/7921153/working/3D/316' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(C)=O)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005042207.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042207.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042207/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042207 none CCN(C(C)=O)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 5, 11, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [48, 40, 31, 40, 43, 43, 14, 31, 29, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 48, 48, 48, 48, 48, 43, 43, 43, 31, 31, 31, 14, 14, 4, 1] 51 rigid atoms, others: [33, 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: 229 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042207 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042207 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042207/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042207 Building REAL250005042208 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042208' /scratch/stefan/7921153/working/building/REAL250005042208 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042208 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042208/0 /scratch/stefan/7921153/working/building/REAL250005042208 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 317) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/317 `/scratch/stefan/7921153/working/3D/317' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C1CC1)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005042208.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042208.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042208/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042208 none CCN(C(=O)C1CC1)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [105, 81, 54, 81, 96, 96, 134, 134, 22, 54, 52, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 105, 105, 105, 105, 105, 134, 134, 134, 134, 134, 54, 54, 54, 22, 22, 8, 1] 167 rigid atoms, others: [37, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 655 number of broken/clashed sets: 80 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042208 none CCN(C(=O)C1CC1)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [30, 19, 8, 1, 8, 1, 1, 1, 19, 37, 37, 37, 73, 129, 129, 129, 134, 134, 134, 134, 134, 30, 30, 30, 30, 30, 1, 1, 1, 1, 1, 37, 37, 37, 73, 73, 129, 134] 167 rigid atoms, others: [3, 5, 6, 7, 26, 27, 28, 29, 30] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 540 number of broken/clashed sets: 80 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042208 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042208 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042208/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042208 Building REAL250005042209 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042209' /scratch/stefan/7921153/working/building/REAL250005042209 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042209 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042209/0 /scratch/stefan/7921153/working/building/REAL250005042209 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 318) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/318 `/scratch/stefan/7921153/working/3D/318' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C1CCC1)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005042209.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042209/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042209 none CCN(C(=O)C1CCC1)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [115, 93, 57, 93, 118, 118, 135, 135, 135, 25, 57, 56, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 115, 115, 115, 115, 115, 135, 135, 135, 135, 135, 135, 135, 57, 57, 57, 25, 25, 8, 1] 146 rigid atoms, others: [40, 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]) total number of confs: 630 number of broken/clashed sets: 67 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042209 none CCN(C(=O)C1CCC1)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [28, 20, 7, 1, 7, 1, 1, 1, 1, 20, 36, 36, 36, 80, 131, 132, 131, 135, 135, 135, 135, 135, 28, 28, 28, 28, 28, 1, 1, 1, 1, 1, 1, 1, 36, 36, 36, 80, 80, 132, 135] 146 rigid atoms, others: [32, 33, 3, 5, 6, 7, 8, 27, 28, 29, 30, 31] set([0, 1, 2, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 542 number of broken/clashed sets: 67 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042209 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042209 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042209/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042209 Building REAL250005042210 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042210' /scratch/stefan/7921153/working/building/REAL250005042210 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042210 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042210/0 /scratch/stefan/7921153/working/building/REAL250005042210 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 319) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/319 `/scratch/stefan/7921153/working/3D/319' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C(N)=O)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005042210.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042210.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042210/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042210 none CCN(C(=O)C(N)=O)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 8, 11, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 4, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [80, 65, 44, 65, 72, 72, 82, 82, 22, 44, 44, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 80, 80, 80, 80, 80, 82, 82, 44, 44, 44, 22, 22, 7, 1] 98 rigid atoms, others: [34, 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]) total number of confs: 394 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042210 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042210 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042210/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042210 Building REAL250005042211 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042211' /scratch/stefan/7921153/working/building/REAL250005042211 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042211 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042211/0 /scratch/stefan/7921153/working/building/REAL250005042211 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 320) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/320 `/scratch/stefan/7921153/working/3D/320' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@H]1C[C@H]1C)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005042211.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042211/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042211 none CCN(C(=O)[C@@H]1C[C@H]1C)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [116, 90, 63, 90, 109, 109, 142, 142, 142, 142, 142, 26, 63, 62, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 116, 116, 116, 116, 116, 142, 142, 142, 142, 142, 63, 63, 63, 26, 26, 8, 1] 175 rigid atoms, others: [40, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 702 number of broken/clashed sets: 74 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042211 none CCN(C(=O)[C@@H]1C[C@H]1C)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [30, 21, 8, 1, 8, 1, 1, 1, 1, 1, 1, 21, 38, 38, 38, 76, 130, 130, 130, 142, 142, 142, 142, 142, 30, 30, 30, 30, 30, 1, 1, 2, 2, 2, 38, 38, 38, 76, 76, 130, 142] 175 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 29, 30] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 543 number of broken/clashed sets: 74 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042211 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042211 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042211/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042211 Building REAL250005042212 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042212' /scratch/stefan/7921153/working/building/REAL250005042212 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042212 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042212/0 /scratch/stefan/7921153/working/building/REAL250005042212 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 321) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/321 `/scratch/stefan/7921153/working/3D/321' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@H]1C[C@@H]1C)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005042212.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042212/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042212 none CCN(C(=O)[C@H]1C[C@@H]1C)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [107, 80, 52, 80, 96, 96, 125, 125, 125, 125, 125, 24, 52, 51, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 107, 107, 107, 107, 107, 125, 125, 125, 125, 125, 52, 52, 52, 23, 23, 8, 1] 157 rigid atoms, others: [40, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 629 number of broken/clashed sets: 63 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042212 none CCN(C(=O)[C@H]1C[C@@H]1C)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [27, 18, 8, 1, 8, 1, 1, 1, 1, 1, 1, 18, 37, 37, 37, 73, 121, 121, 121, 125, 125, 125, 125, 125, 27, 27, 27, 27, 27, 1, 1, 2, 2, 2, 37, 37, 37, 73, 73, 121, 125] 157 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 29, 30] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 525 number of broken/clashed sets: 63 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042212 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042212 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042212/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042212 Building REAL250005042213 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042213' /scratch/stefan/7921153/working/building/REAL250005042213 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042213 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042213/0 /scratch/stefan/7921153/working/building/REAL250005042213 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 322) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/322 `/scratch/stefan/7921153/working/3D/322' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)CO)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005042213.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042213.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042213/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042213 none CCN(C(=O)CO)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 564 conformations in input total number of sets (complete confs): 564 using faster count positions algorithm for large data unique positions, atoms: [150, 119, 75, 119, 139, 139, 170, 31, 75, 73, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 150, 150, 150, 150, 150, 170, 170, 510, 75, 75, 75, 31, 31, 7, 1] 564 rigid atoms, others: [34, 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]) total number of confs: 1391 number of broken/clashed sets: 354 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042213 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042213 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042213/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042213 Building REAL250005042214 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042214' /scratch/stefan/7921153/working/building/REAL250005042214 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042214 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042214/0 /scratch/stefan/7921153/working/building/REAL250005042214 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 323) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/323 `/scratch/stefan/7921153/working/3D/323' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C1CCO1)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005042214.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042214.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042214/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042214 none CCN(C(=O)C1CCO1)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [111, 90, 59, 90, 106, 106, 126, 126, 126, 26, 59, 56, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 111, 111, 111, 111, 111, 126, 126, 126, 126, 126, 59, 59, 59, 26, 26, 8, 1] 144 rigid atoms, others: [38, 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]) total number of confs: 620 number of broken/clashed sets: 64 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042214 none CCN(C(=O)C1CCO1)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [23, 17, 6, 1, 6, 1, 1, 1, 1, 17, 31, 31, 31, 68, 116, 116, 116, 126, 126, 126, 126, 126, 23, 23, 23, 23, 23, 1, 1, 1, 1, 1, 31, 31, 31, 68, 68, 116, 126] 144 rigid atoms, others: [3, 5, 6, 7, 8, 27, 28, 29, 30, 31] set([0, 1, 2, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 474 number of broken/clashed sets: 64 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042214 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042214 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042214/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042214 Building REAL250005042215 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042215' /scratch/stefan/7921153/working/building/REAL250005042215 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042215 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042215/0 /scratch/stefan/7921153/working/building/REAL250005042215 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 324) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/324 `/scratch/stefan/7921153/working/3D/324' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C1COC1)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005042215.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042215.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042215/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042215 none CCN(C(=O)C1COC1)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [128, 100, 61, 100, 131, 131, 154, 154, 154, 23, 61, 58, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 128, 128, 128, 128, 128, 154, 154, 154, 154, 154, 61, 61, 61, 23, 23, 7, 1] 172 rigid atoms, others: [38, 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]) total number of confs: 737 number of broken/clashed sets: 92 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042215 none CCN(C(=O)C1COC1)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [37, 26, 8, 1, 8, 1, 1, 1, 1, 26, 48, 48, 48, 97, 152, 152, 152, 154, 154, 154, 154, 154, 37, 37, 37, 37, 37, 1, 1, 1, 1, 1, 48, 48, 48, 97, 97, 152, 154] 172 rigid atoms, others: [3, 5, 6, 7, 8, 27, 28, 29, 30, 31] set([0, 1, 2, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 656 number of broken/clashed sets: 92 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042215 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042215 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042215/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042215 Building REAL250005042216 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042216' /scratch/stefan/7921153/working/building/REAL250005042216 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042216 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042216/0 /scratch/stefan/7921153/working/building/REAL250005042216 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 325) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/325 `/scratch/stefan/7921153/working/3D/325' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C=CCO)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005042216.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042216.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042216/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042216 none CCN(C(=O)C=CCO)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 5, 12, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [128, 90, 50, 90, 107, 107, 171, 171, 193, 24, 50, 50, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 128, 128, 128, 128, 128, 171, 171, 193, 193, 579, 50, 50, 50, 24, 24, 5, 1] 603 rigid atoms, others: [38, 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]) total number of confs: 1539 number of broken/clashed sets: 270 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042216 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042216 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042216/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042216 Building REAL250005042217 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042217' /scratch/stefan/7921153/working/building/REAL250005042217 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042217 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042217/0 /scratch/stefan/7921153/working/building/REAL250005042217 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 326) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/326 `/scratch/stefan/7921153/working/3D/326' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC=CC(=O)N(CC)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005042217.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042217/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042217 none CCC=CC(=O)N(CC)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 144, 144, 85, 72, 85, 39, 72, 104, 17, 39, 38, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 183, 183, 183, 183, 183, 144, 144, 104, 104, 104, 104, 104, 39, 39, 39, 17, 17, 4, 1] 201 rigid atoms, others: [40, 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]) total number of confs: 934 number of broken/clashed sets: 84 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042217 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042217 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042217/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042217 Building REAL250005042218 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042218' /scratch/stefan/7921153/working/building/REAL250005042218 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042218 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042218/0 /scratch/stefan/7921153/working/building/REAL250005042218 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 327) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/327 `/scratch/stefan/7921153/working/3D/327' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCC(=O)N(CC)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005042218.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042218/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042218 none C#CCCC(=O)N(CC)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 157, 119, 88, 119, 51, 88, 116, 17, 51, 49, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 167, 167, 167, 157, 157, 116, 116, 116, 116, 116, 51, 51, 51, 17, 17, 4, 1] 201 rigid atoms, others: [38, 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]) total number of confs: 851 number of broken/clashed sets: 95 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042218 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042218 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042218/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042218 Building REAL250005042219 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042219' /scratch/stefan/7921153/working/building/REAL250005042219 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042219 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042219/0 /scratch/stefan/7921153/working/building/REAL250005042219 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 328) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/328 `/scratch/stefan/7921153/working/3D/328' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(O)C(=O)N(CC)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005042219.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042219.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042219/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042219 none C=CC(O)C(=O)N(CC)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 321 conformations in input total number of sets (complete confs): 321 using faster count positions algorithm for large data unique positions, atoms: [98, 95, 77, 95, 62, 77, 39, 62, 75, 19, 39, 39, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 98, 98, 98, 95, 285, 75, 75, 75, 75, 75, 39, 39, 39, 19, 19, 5, 1] 321 rigid atoms, others: [38, 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]) total number of confs: 771 number of broken/clashed sets: 218 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042219 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042219 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042219/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042219 Building REAL250005042220 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042220' /scratch/stefan/7921153/working/building/REAL250005042220 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042220 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042220/0 /scratch/stefan/7921153/working/building/REAL250005042220 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 329) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/329 `/scratch/stefan/7921153/working/3D/329' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C(C)O)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005042220.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042220.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042220/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042220 none CCN(C(=O)C(C)O)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 12, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 384 conformations in input total number of sets (complete confs): 384 using faster count positions algorithm for large data unique positions, atoms: [100, 82, 49, 82, 99, 99, 115, 115, 19, 49, 48, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 100, 100, 100, 100, 100, 115, 115, 115, 115, 345, 49, 49, 49, 19, 19, 6, 1] 384 rigid atoms, others: [37, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 905 number of broken/clashed sets: 248 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042220 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042220 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042220/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042220 Building REAL250005042221 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042221' /scratch/stefan/7921153/working/building/REAL250005042221 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042221 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042221/0 /scratch/stefan/7921153/working/building/REAL250005042221 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 330) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/330 `/scratch/stefan/7921153/working/3D/330' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C(C)=O)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005042221.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042221.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042221/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042221 none CCN(C(=O)C(C)=O)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.3', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 5, 11, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [84, 67, 43, 67, 79, 79, 95, 95, 23, 43, 42, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 84, 84, 84, 84, 84, 95, 95, 95, 43, 43, 43, 23, 23, 9, 1] 114 rigid atoms, others: [35, 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]) total number of confs: 459 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042221 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042221 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042221/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042221 Building REAL250005042222 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042222' /scratch/stefan/7921153/working/building/REAL250005042222 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042222 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042222/0 /scratch/stefan/7921153/working/building/REAL250005042222 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 331) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/331 `/scratch/stefan/7921153/working/3D/331' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=C(F)C(=O)N(CC)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005042222.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042222.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042222/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042222 none CC=C(F)C(=O)N(CC)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 15, 1, 11, 8, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [191, 191, 137, 191, 101, 137, 57, 101, 130, 24, 57, 56, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 191, 191, 191, 191, 130, 130, 130, 130, 130, 57, 57, 57, 24, 24, 6, 1] 201 rigid atoms, others: [37, 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]) total number of confs: 845 number of broken/clashed sets: 85 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042222 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042222 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042222/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042222 Building REAL250005042223 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042223' /scratch/stefan/7921153/working/building/REAL250005042223 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042223 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042223/0 /scratch/stefan/7921153/working/building/REAL250005042223 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 332) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/332 `/scratch/stefan/7921153/working/3D/332' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C(C)CO)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005042223.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042223.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042223/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042223 none CCN(C(=O)C(C)CO)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 357 conformations in input total number of sets (complete confs): 357 using faster count positions algorithm for large data unique positions, atoms: [91, 70, 46, 70, 91, 91, 109, 109, 112, 16, 46, 44, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 91, 91, 91, 91, 91, 109, 109, 109, 109, 112, 112, 336, 46, 46, 46, 16, 16, 4, 1] 357 rigid atoms, others: [40, 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]) total number of confs: 922 number of broken/clashed sets: 156 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042223 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042223 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042223/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042223 Building REAL250005042224 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042224' /scratch/stefan/7921153/working/building/REAL250005042224 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042224 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042224/0 /scratch/stefan/7921153/working/building/REAL250005042224 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 333) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/333 `/scratch/stefan/7921153/working/3D/333' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C1=CCC1)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005042224.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042224.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042224/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042224 none CCN(C(=O)C1=CCC1)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [106, 85, 50, 85, 102, 102, 113, 113, 113, 24, 50, 49, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 106, 106, 106, 106, 106, 113, 113, 113, 113, 113, 50, 50, 50, 24, 24, 9, 1] 123 rigid atoms, others: [38, 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]) total number of confs: 519 number of broken/clashed sets: 56 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042224 none CCN(C(=O)C1=CCC1)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [33, 23, 9, 1, 9, 1, 1, 1, 1, 23, 39, 39, 39, 72, 109, 109, 109, 113, 113, 113, 113, 113, 33, 33, 33, 33, 33, 1, 1, 1, 1, 1, 39, 39, 39, 72, 72, 109, 113] 123 rigid atoms, others: [3, 5, 6, 7, 8, 27, 28, 29, 30, 31] set([0, 1, 2, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 490 number of broken/clashed sets: 56 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042224 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042224 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042224/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042224 Building REAL250005042225 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042225' /scratch/stefan/7921153/working/building/REAL250005042225 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042225 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042225/0 /scratch/stefan/7921153/working/building/REAL250005042225 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 334) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/334 `/scratch/stefan/7921153/working/3D/334' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=CC(=O)N(CC)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005042225.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042225.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042225/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042225 none CC=CC(=O)N(CC)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [147, 147, 114, 94, 114, 58, 94, 116, 26, 58, 58, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 147, 147, 147, 147, 147, 116, 116, 116, 116, 116, 58, 58, 58, 26, 26, 9, 1] 152 rigid atoms, others: [37, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 652 number of broken/clashed sets: 68 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042225 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042225 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042225/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042225 Building REAL250005042226 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042226' /scratch/stefan/7921153/working/building/REAL250005042226 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042226 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042226/0 /scratch/stefan/7921153/working/building/REAL250005042226 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 335) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/335 `/scratch/stefan/7921153/working/3D/335' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C=CCF)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005042226.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042226.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042226/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042226 none CCN(C(=O)C=CCF)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'F', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 5, 15, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [107, 79, 50, 79, 100, 100, 172, 172, 191, 19, 50, 49, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 107, 107, 107, 107, 107, 172, 172, 191, 191, 50, 50, 50, 19, 19, 6, 1] 201 rigid atoms, others: [37, 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]) total number of confs: 876 number of broken/clashed sets: 70 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042226 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042226 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042226/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042226 Building REAL250005042227 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042227' /scratch/stefan/7921153/working/building/REAL250005042227 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types Protomer extracton resulted in 0 protomers Marking REAL250005042227 as failed and skipping /scratch/stefan/7921153/working /scratch/stefan/7921153 `/scratch/stefan/7921153/working/building/REAL250005042227' -> `/scratch/stefan/7921153/failed/REAL250005042227' Building REAL250005042228 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042228' /scratch/stefan/7921153/working/building/REAL250005042228 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042228 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042228/0 /scratch/stefan/7921153/working/building/REAL250005042228 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 336) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/336 `/scratch/stefan/7921153/working/3D/336' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@H](C)O)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005042228.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042228.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042228/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042228 none CCN(C(=O)[C@H](C)O)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 381 conformations in input total number of sets (complete confs): 381 using faster count positions algorithm for large data unique positions, atoms: [98, 79, 51, 79, 96, 96, 115, 115, 115, 22, 51, 50, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 98, 98, 98, 98, 98, 115, 115, 115, 345, 51, 51, 51, 22, 22, 7, 1] 381 rigid atoms, others: [37, 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]) total number of confs: 930 number of broken/clashed sets: 233 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042228 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042228 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042228/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042228 Building REAL250005042229 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042229' /scratch/stefan/7921153/working/building/REAL250005042229 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042229 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042229/0 /scratch/stefan/7921153/working/building/REAL250005042229 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 337) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/337 `/scratch/stefan/7921153/working/3D/337' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C=NOC)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005042229.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042229.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042229/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042229 none CCN(C(=O)C=NOC)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 8, 12, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [120, 87, 47, 87, 112, 112, 159, 159, 163, 18, 47, 45, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 120, 120, 120, 120, 120, 159, 163, 163, 163, 47, 47, 47, 18, 18, 4, 1] 201 rigid atoms, others: [37, 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]) total number of confs: 791 number of broken/clashed sets: 88 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042229 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042229 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042229/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042229 Building REAL250005042230 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042230' /scratch/stefan/7921153/working/building/REAL250005042230 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042230 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042230/0 /scratch/stefan/7921153/working/building/REAL250005042230 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 338) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/338 `/scratch/stefan/7921153/working/3D/338' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@H]1C[C@H]1C)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005042230.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042230/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042230 none CCN(C(=O)[C@@H]1C[C@H]1C)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [116, 90, 63, 90, 109, 109, 142, 142, 142, 142, 142, 26, 63, 62, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 116, 116, 116, 116, 116, 142, 142, 142, 142, 142, 63, 63, 63, 26, 26, 8, 1] 175 rigid atoms, others: [40, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 702 number of broken/clashed sets: 74 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042230 none CCN(C(=O)[C@@H]1C[C@H]1C)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [30, 21, 8, 1, 8, 1, 1, 1, 1, 1, 1, 21, 38, 38, 38, 76, 130, 130, 130, 142, 142, 142, 142, 142, 30, 30, 30, 30, 30, 1, 1, 2, 2, 2, 38, 38, 38, 76, 76, 130, 142] 175 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 29, 30] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 543 number of broken/clashed sets: 74 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042230 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042230 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042230/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042230 Building REAL250005042231 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042231' /scratch/stefan/7921153/working/building/REAL250005042231 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042231 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042231/0 /scratch/stefan/7921153/working/building/REAL250005042231 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 339) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/339 `/scratch/stefan/7921153/working/3D/339' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C(C)CC(=O)N(CC)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005042231.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042231/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042231 none C=C(C)CC(=O)N(CC)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 176, 183, 103, 79, 103, 48, 79, 105, 17, 48, 47, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 183, 183, 183, 183, 183, 176, 176, 105, 105, 105, 105, 105, 48, 48, 48, 17, 17, 5, 1] 201 rigid atoms, others: [40, 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]) total number of confs: 917 number of broken/clashed sets: 110 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042231 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042231 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042231/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042231 Building REAL250005042232 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042232' /scratch/stefan/7921153/working/building/REAL250005042232 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042232 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042232/0 /scratch/stefan/7921153/working/building/REAL250005042232 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 340) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/340 `/scratch/stefan/7921153/working/3D/340' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC(=O)N(CC)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005042232.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042232.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042232/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042232 none C=CCC(=O)N(CC)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 174, 112, 89, 112, 55, 89, 114, 19, 55, 54, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 180, 180, 180, 174, 174, 114, 114, 114, 114, 114, 55, 55, 55, 19, 19, 5, 1] 201 rigid atoms, others: [37, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 922 number of broken/clashed sets: 98 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042232 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042232 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042232/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042232 Building REAL250005042233 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042233' /scratch/stefan/7921153/working/building/REAL250005042233 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005042233 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042233/0 /scratch/stefan/7921153/working/building/REAL250005042233 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 341) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/341 `/scratch/stefan/7921153/working/3D/341' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C[NH+](C)C)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005042233.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042233/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042233 none CCN(C(=O)C[NH+](C)C)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 9, 6, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [15, 13, 12, 13, 13, 13, 13, 13, 13, 13, 7, 12, 12, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 13, 13, 13, 13, 13, 13, 13, 13, 12, 12, 12, 7, 7, 4, 1] 15 rigid atoms, others: [42, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 64 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042233 /scratch/stefan/7921153/working /scratch/stefan/7921153 mkdir: created directory `1' /scratch/stefan/7921153/working/building/REAL250005042233/1 /scratch/stefan/7921153/working/building/REAL250005042233 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 1 (index: 342) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/342 `/scratch/stefan/7921153/working/3D/342' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)CN(C)C)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005042233.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005042233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042233/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.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: REAL250005042233 none CCN(C(=O)CN(C)C)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 10, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 78, 47, 78, 104, 104, 166, 176, 176, 19, 47, 46, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 101, 101, 101, 101, 101, 166, 166, 176, 176, 176, 176, 176, 176, 47, 47, 47, 19, 19, 4, 1] 201 rigid atoms, others: [41, 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: 876 number of broken/clashed sets: 112 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042233 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042233 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 1: /scratch/stefan/7921153/working/building/REAL250005042233/1.* 0: /scratch/stefan/7921153/working/building/REAL250005042233/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042233 Building REAL250005042234 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042234' /scratch/stefan/7921153/working/building/REAL250005042234 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042234 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042234/0 /scratch/stefan/7921153/working/building/REAL250005042234 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 343) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/343 `/scratch/stefan/7921153/working/3D/343' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)CC#N)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005042234.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042234/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042234 none CCN(C(=O)CC#N)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.1', 'N.1', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 1, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 100, 59, 100, 140, 140, 181, 181, 23, 59, 57, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 124, 124, 124, 124, 124, 181, 181, 59, 59, 59, 23, 23, 7, 1] 201 rigid atoms, others: [34, 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]) total number of confs: 855 number of broken/clashed sets: 108 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042234 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042234 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042234/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042234 Building REAL250005042235 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042235' /scratch/stefan/7921153/working/building/REAL250005042235 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042235 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042235/0 /scratch/stefan/7921153/working/building/REAL250005042235 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 344) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/344 `/scratch/stefan/7921153/working/3D/344' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C1CC1F)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005042235.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042235/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042235 none CCN(C(=O)C1CC1F)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 5, 15, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 192 conformations in input total number of sets (complete confs): 192 using faster count positions algorithm for large data unique positions, atoms: [121, 94, 59, 94, 119, 119, 165, 165, 165, 24, 59, 57, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 121, 121, 121, 121, 121, 165, 165, 165, 165, 59, 59, 59, 24, 24, 8, 1] 192 rigid atoms, others: [37, 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]) total number of confs: 768 number of broken/clashed sets: 101 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042235 none CCN(C(=O)C1CC1F)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 5, 15, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 192 conformations in input total number of sets (complete confs): 192 using faster count positions algorithm for large data unique positions, atoms: [42, 27, 8, 1, 8, 1, 1, 1, 1, 27, 47, 47, 47, 100, 158, 158, 158, 165, 165, 165, 165, 165, 42, 42, 42, 42, 42, 1, 1, 1, 1, 47, 47, 47, 100, 100, 158, 165] 192 rigid atoms, others: [3, 5, 6, 7, 8, 27, 28, 29, 30] set([0, 1, 2, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 689 number of broken/clashed sets: 101 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042235 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042235 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042235/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042235 Building REAL250005042236 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042236' /scratch/stefan/7921153/working/building/REAL250005042236 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042236 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042236/0 /scratch/stefan/7921153/working/building/REAL250005042236 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 345) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/345 `/scratch/stefan/7921153/working/3D/345' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)CCF)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005042236.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042236.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042236/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042236 none CCN(C(=O)CCF)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 15, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [131, 101, 60, 101, 128, 128, 178, 179, 22, 60, 57, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 131, 131, 131, 131, 131, 178, 178, 179, 179, 60, 60, 60, 22, 22, 7, 1] 201 rigid atoms, others: [36, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 909 number of broken/clashed sets: 85 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042236 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042236 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042236/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042236 Building REAL250005042237 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042237' /scratch/stefan/7921153/working/building/REAL250005042237 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042237 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042237/0 /scratch/stefan/7921153/working/building/REAL250005042237 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 346) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/346 `/scratch/stefan/7921153/working/3D/346' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@H](C)OC)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005042237.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042237.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042237/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042237 none CCN(C(=O)[C@@H](C)OC)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 108 conformations in input total number of sets (complete confs): 108 using faster count positions algorithm for large data unique positions, atoms: [81, 64, 42, 64, 78, 78, 93, 93, 93, 99, 17, 42, 42, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 81, 81, 81, 81, 81, 93, 93, 93, 99, 99, 99, 42, 42, 42, 17, 17, 4, 1] 108 rigid atoms, others: [40, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 495 number of broken/clashed sets: 68 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042237 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042237 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042237/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042237 Building REAL250005042238 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042238' /scratch/stefan/7921153/working/building/REAL250005042238 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042238 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042238/0 /scratch/stefan/7921153/working/building/REAL250005042238 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 347) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/347 `/scratch/stefan/7921153/working/3D/347' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@H](C)O)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005042238.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042238/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042238 none CCN(C(=O)[C@@H](C)O)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 384 conformations in input total number of sets (complete confs): 384 using faster count positions algorithm for large data unique positions, atoms: [100, 82, 49, 82, 99, 99, 115, 115, 115, 19, 49, 48, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 100, 100, 100, 100, 100, 115, 115, 115, 345, 49, 49, 49, 19, 19, 6, 1] 384 rigid atoms, others: [37, 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]) total number of confs: 905 number of broken/clashed sets: 248 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042238 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042238 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042238/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042238 Building REAL250005042239 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042239' /scratch/stefan/7921153/working/building/REAL250005042239 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042239 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042239/0 /scratch/stefan/7921153/working/building/REAL250005042239 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 348) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/348 `/scratch/stefan/7921153/working/3D/348' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C1CC1C(=O)N(CC)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005042239.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042239.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042239/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042239 none C=C1CC1C(=O)N(CC)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 122 conformations in input total number of sets (complete confs): 122 using faster count positions algorithm for large data unique positions, atoms: [107, 107, 107, 84, 68, 84, 44, 68, 86, 22, 44, 44, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 107, 107, 107, 107, 107, 86, 86, 86, 86, 86, 44, 44, 44, 22, 22, 9, 1] 122 rigid atoms, others: [38, 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]) total number of confs: 500 number of broken/clashed sets: 49 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042239 none C=C1CC1C(=O)N(CC)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 122 conformations in input total number of sets (complete confs): 122 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 8, 8, 19, 25, 19, 35, 35, 35, 62, 103, 103, 103, 107, 107, 107, 107, 107, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 35, 35, 35, 62, 62, 103, 107] 122 rigid atoms, others: [0, 1, 2, 3, 4, 22, 23, 24, 25, 26] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 434 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042239 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042239 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042239/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042239 Building REAL250005042240 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042240' /scratch/stefan/7921153/working/building/REAL250005042240 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042240 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042240/0 /scratch/stefan/7921153/working/building/REAL250005042240 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 349) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/349 `/scratch/stefan/7921153/working/3D/349' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C1C=C1C)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005042240.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042240.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042240/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042240 none CCN(C(=O)C1C=C1C)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 1, 1, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [96, 72, 46, 72, 91, 91, 117, 117, 117, 21, 46, 46, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 96, 96, 96, 96, 96, 117, 117, 117, 117, 117, 46, 46, 46, 21, 21, 8, 1] 136 rigid atoms, others: [38, 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]) total number of confs: 574 number of broken/clashed sets: 50 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042240 none CCN(C(=O)C1C=C1C)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 1, 1, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [27, 19, 8, 1, 8, 1, 1, 1, 1, 19, 35, 35, 35, 68, 114, 114, 114, 117, 117, 117, 117, 117, 27, 27, 27, 27, 27, 1, 1, 2, 2, 2, 35, 35, 35, 68, 68, 114, 117] 136 rigid atoms, others: [3, 5, 6, 7, 8, 27, 28] set([0, 1, 2, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 487 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042240 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042240 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042240/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042240 Building REAL250005042241 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042241' /scratch/stefan/7921153/working/building/REAL250005042241 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042241 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042241/0 /scratch/stefan/7921153/working/building/REAL250005042241 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 350) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/350 `/scratch/stefan/7921153/working/3D/350' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(=O)N(CC)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005042241.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042241.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042241/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042241 none C=CC(=O)N(CC)[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [95, 83, 71, 83, 47, 71, 87, 22, 47, 44, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 95, 95, 95, 87, 87, 87, 87, 87, 47, 47, 47, 22, 22, 7, 1] 98 rigid atoms, others: [34, 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]) total number of confs: 462 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042241 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042241 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042241/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042241 Building REAL250005042242 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042242' /scratch/stefan/7921153/working/building/REAL250005042242 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042242 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042242/0 /scratch/stefan/7921153/working/building/REAL250005042242 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 351) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/351 `/scratch/stefan/7921153/working/3D/351' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N1CCCC[C@@H]1CN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005042242.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042242.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042242/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042242 none CCC(=O)N1CCCC[C@@H]1CN(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 69, 63, 69, 63, 63, 63, 63, 63, 46, 63, 31, 11, 31, 1, 11, 1, 1, 1, 1, 1, 1, 74, 74, 74, 74, 74, 63, 63, 63, 63, 63, 63, 63, 63, 46, 46, 31, 31, 31, 1] 74 rigid atoms, others: [40, 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]) total number of confs: 269 number of broken/clashed sets: 12 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042242 none CCC(=O)N1CCCC[C@@H]1CN(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [11, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 4, 12, 12, 38, 38, 63, 63, 63, 63, 63, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12, 12, 12, 63] 74 rigid atoms, others: [32, 33, 2, 4, 5, 6, 7, 8, 9, 10, 11, 34, 27, 28, 29, 30, 31] set([0, 1, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 35, 36, 37, 38, 39, 40]) total number of confs: 180 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042242 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042242 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042242/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042242 Building REAL250005042243 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042243' /scratch/stefan/7921153/working/building/REAL250005042243 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042243 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042243/0 /scratch/stefan/7921153/working/building/REAL250005042243 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 352) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/352 `/scratch/stefan/7921153/working/3D/352' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCCC[C@@H]1CN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005042243.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042243.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042243/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042243 none CC(=O)N1CCCC[C@@H]1CN(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 13, 13, 13, 13, 12, 13, 11, 6, 11, 1, 6, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 12, 12, 11, 11, 11, 1] 13 rigid atoms, others: [37, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 39 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042243 none CC(=O)N1CCCC[C@@H]1CN(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 4, 8, 8, 13, 13, 13, 13, 13, 13, 13, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 8, 8, 8, 13] 13 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 32, 2, 34, 36, 37, 35, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23]) total number of confs: 49 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042243 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042243 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042243/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042243 Building REAL250005042244 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042244' /scratch/stefan/7921153/working/building/REAL250005042244 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042244 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042244/0 /scratch/stefan/7921153/working/building/REAL250005042244 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 353) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/353 `/scratch/stefan/7921153/working/3D/353' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H]1CCCCN1C(=O)CO)C(=O)C1=CC(=O)[N-]O1) `REAL250005042244.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042244/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042244 none CN(C[C@H]1CCCCN1C(=O)CO)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [10, 5, 10, 13, 16, 16, 16, 16, 16, 16, 16, 18, 18, 22, 1, 5, 1, 1, 1, 1, 1, 1, 10, 10, 10, 13, 13, 16, 16, 16, 16, 16, 16, 16, 16, 22, 22, 66, 1] 66 rigid atoms, others: [38, 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]) total number of confs: 150 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042244 none CN(C[C@H]1CCCCN1C(=O)CO)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [8, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 8, 12, 12, 16, 16, 16, 16, 16, 8, 8, 8, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 21, 16] 66 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 34, 27, 28, 29, 30, 31] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 35, 36, 37, 38]) total number of confs: 93 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042244 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042244 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042244/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042244 Building REAL250005042245 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042245' /scratch/stefan/7921153/working/building/REAL250005042245 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042245 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042245/0 /scratch/stefan/7921153/working/building/REAL250005042245 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 354) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/354 `/scratch/stefan/7921153/working/3D/354' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N(C)C[C@H]1CCCCN1C(=O)C1=CC(=O)[N-]O1) `REAL250005042245.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042245.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042245/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042245 none CCC(=O)N(C)C[C@H]1CCCCN1C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 49, 35, 49, 20, 35, 14, 14, 14, 14, 14, 14, 14, 10, 1, 10, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 35, 35, 35, 20, 20, 14, 14, 14, 14, 14, 14, 14, 14, 1] 50 rigid atoms, others: [40, 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]) total number of confs: 167 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042245 none CCC(=O)N(C)C[C@H]1CCCCN1C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [31, 26, 11, 26, 4, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 14, 14, 14, 14, 14, 31, 31, 31, 31, 31, 11, 11, 11, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 14] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 13, 14, 39, 38] set([0, 1, 2, 3, 4, 5, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 40]) total number of confs: 127 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042245 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042245 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042245/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042245 Building REAL250005042246 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042246' /scratch/stefan/7921153/working/building/REAL250005042246 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042246 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042246/0 /scratch/stefan/7921153/working/building/REAL250005042246 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 355) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/355 `/scratch/stefan/7921153/working/3D/355' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N(C)C[C@H]1CCCCN1C(=O)C1=CC(=O)[N-]O1) `REAL250005042246.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042246/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042246 none CC(=O)N(C)C[C@H]1CCCCN1C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 31, 37, 22, 31, 15, 15, 15, 15, 15, 15, 15, 11, 1, 11, 1, 1, 1, 1, 1, 1, 37, 37, 37, 31, 31, 31, 22, 22, 15, 15, 15, 15, 15, 15, 15, 15, 1] 37 rigid atoms, others: [37, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 129 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042246 none CC(=O)N(C)C[C@H]1CCCCN1C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [16, 10, 16, 4, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 15, 15, 15, 15, 15, 16, 16, 16, 10, 10, 10, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 15] 37 rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 12, 13, 29, 30, 31] set([0, 1, 2, 3, 4, 37, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 77 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042246 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042246 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042246/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042246 Building REAL250005042247 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042247' /scratch/stefan/7921153/working/building/REAL250005042247 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042247 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042247/0 /scratch/stefan/7921153/working/building/REAL250005042247 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 356) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/356 `/scratch/stefan/7921153/working/3D/356' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H]1CCCCN1C(=O)C1=CC(=O)[N-]O1)C(=O)CO) `REAL250005042247.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042247/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042247 none CN(C[C@H]1CCCCN1C(=O)C1=CC(=O)[N-]O1)C(=O)CO NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [36, 22, 16, 16, 16, 16, 16, 16, 16, 11, 1, 11, 1, 1, 1, 1, 1, 1, 36, 47, 47, 48, 36, 36, 36, 22, 22, 16, 16, 16, 16, 16, 16, 16, 16, 1, 48, 48, 144] 144 rigid atoms, others: [35, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38]) total number of confs: 305 number of broken/clashed sets: 31 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042247 none CN(C[C@H]1CCCCN1C(=O)C1=CC(=O)[N-]O1)C(=O)CO NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [12, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 16, 16, 16, 16, 16, 12, 21, 21, 35, 12, 12, 12, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 16, 35, 35, 105] 144 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 34, 27, 28, 29, 30, 31] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 35, 36, 37, 38]) total number of confs: 272 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042247 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042247 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042247/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042247 Building REAL250005042248 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042248' /scratch/stefan/7921153/working/building/REAL250005042248 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042248 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042248/0 /scratch/stefan/7921153/working/building/REAL250005042248 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 357) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/357 `/scratch/stefan/7921153/working/3D/357' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(=O)N(C)C[C@H]1CCCCN1C(=O)C1=CC(=O)[N-]O1) `REAL250005042248.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042248/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042248 none C=CC(=O)N(C)C[C@H]1CCCCN1C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 31, 47, 20, 31, 14, 14, 14, 14, 14, 14, 14, 10, 1, 10, 1, 1, 1, 1, 1, 1, 47, 47, 47, 31, 31, 31, 20, 20, 14, 14, 14, 14, 14, 14, 14, 14, 1] 47 rigid atoms, others: [38, 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]) total number of confs: 156 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042248 none C=CC(=O)N(C)C[C@H]1CCCCN1C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [31, 23, 11, 23, 4, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 14, 14, 14, 14, 14, 31, 31, 31, 11, 11, 11, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 14] 47 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 13, 14, 30, 31] set([0, 1, 2, 3, 4, 5, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 38]) total number of confs: 120 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042248 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042248 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042248/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042248 Building REAL250005042249 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042249' /scratch/stefan/7921153/working/building/REAL250005042249 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042249 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042249/0 /scratch/stefan/7921153/working/building/REAL250005042249 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 358) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/358 `/scratch/stefan/7921153/working/3D/358' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)NCCC1=CCN(C(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005042249.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042249/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042249 none CCC(=O)NCCC1=CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 136, 136, 136, 91, 61, 21, 21, 21, 21, 8, 1, 8, 1, 1, 1, 1, 1, 1, 21, 21, 198, 201, 201, 201, 201, 136, 91, 91, 61, 61, 21, 21, 21, 1, 21, 21, 21, 21] 201 rigid atoms, others: [34, 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, 35, 36, 37, 38]) total number of confs: 891 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042249 none CCC(=O)NCCC1=CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 37, 37, 37, 12, 7, 1, 1, 1, 1, 1, 1, 7, 7, 21, 21, 21, 21, 21, 1, 1, 90, 91, 91, 91, 91, 37, 12, 12, 7, 7, 1, 1, 1, 21, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 35, 36, 37, 6, 7, 8, 9, 10, 11, 19, 20, 38, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34]) total number of confs: 387 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042249 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042249 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042249/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042249 Building REAL250005042250 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042250' /scratch/stefan/7921153/working/building/REAL250005042250 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042250 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042250/0 /scratch/stefan/7921153/working/building/REAL250005042250 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 359) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/359 `/scratch/stefan/7921153/working/3D/359' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCCC1=CCN(C(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005042250.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042250.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042250/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042250 none CC(=O)NCCC1=CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 103, 36, 36, 36, 36, 11, 1, 11, 1, 1, 1, 1, 1, 1, 36, 36, 201, 201, 201, 201, 145, 145, 103, 103, 36, 36, 36, 1, 36, 36, 36, 36] 201 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35]) total number of confs: 757 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042250 none CC(=O)NCCC1=CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 16, 8, 1, 1, 1, 1, 1, 1, 7, 7, 36, 36, 36, 36, 36, 1, 1, 61, 61, 61, 61, 16, 16, 8, 8, 1, 1, 1, 36, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 10, 18, 19, 28, 29, 30] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 234 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042250 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042250 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042250/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042250 Building REAL250005042251 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042251' /scratch/stefan/7921153/working/building/REAL250005042251 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042251 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042251/0 /scratch/stefan/7921153/working/building/REAL250005042251 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 360) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/360 `/scratch/stefan/7921153/working/3D/360' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CO)NCCC1=CCN(C(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005042251.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042251/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042251 none O=C(CO)NCCC1=CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [199, 199, 199, 201, 120, 76, 23, 23, 23, 23, 10, 1, 10, 1, 1, 1, 1, 1, 1, 23, 23, 201, 201, 603, 199, 120, 120, 76, 76, 23, 23, 23, 1, 23, 23, 23, 23] 603 rigid atoms, others: [32, 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, 33, 34, 35, 36]) total number of confs: 1348 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042251 none O=C(CO)NCCC1=CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [56, 56, 56, 88, 14, 8, 1, 1, 1, 1, 1, 1, 7, 7, 23, 23, 23, 23, 23, 1, 1, 88, 88, 264, 56, 14, 14, 8, 8, 1, 1, 1, 23, 1, 1, 1, 1] 603 rigid atoms, others: [33, 34, 35, 36, 6, 7, 8, 9, 10, 11, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 32]) total number of confs: 627 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042251 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042251 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042251/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042251 Building REAL250005042252 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042252' /scratch/stefan/7921153/working/building/REAL250005042252 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042252 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042252/0 /scratch/stefan/7921153/working/building/REAL250005042252 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 361) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/361 `/scratch/stefan/7921153/working/3D/361' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N1CC=C(CCNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005042252.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042252.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042252/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042252 none CCC(=O)N1CC=C(CCNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 198, 109, 198, 109, 109, 109, 49, 27, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 109, 109, 201, 201, 201, 201, 201, 109, 109, 109, 49, 49, 27, 27, 6, 1, 109, 109, 109, 109] 201 rigid atoms, others: [34, 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, 35, 36, 37, 38]) total number of confs: 584 number of broken/clashed sets: 24 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042252 none CCC(=O)N1CC=C(CCNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 6, 1, 6, 1, 1, 1, 1, 1, 9, 19, 86, 86, 86, 109, 109, 109, 109, 109, 1, 1, 19, 19, 19, 19, 19, 1, 1, 1, 9, 9, 19, 19, 86, 109, 1, 1, 1, 1] 201 rigid atoms, others: [2, 35, 4, 5, 6, 7, 8, 38, 19, 20, 36, 26, 27, 28, 37] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34]) total number of confs: 361 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042252 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042252 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042252/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042252 Building REAL250005042253 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042253' /scratch/stefan/7921153/working/building/REAL250005042253 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042253 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042253/0 /scratch/stefan/7921153/working/building/REAL250005042253 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 362) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/362 `/scratch/stefan/7921153/working/3D/362' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CC=C(CCNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005042253.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042253.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042253/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042253 none CC(=O)N1CC=C(CCNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [99, 77, 99, 77, 77, 77, 40, 24, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 77, 77, 99, 99, 99, 77, 77, 77, 40, 40, 24, 24, 7, 1, 77, 77, 77, 77] 99 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35]) total number of confs: 316 number of broken/clashed sets: 16 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042253 none CC(=O)N1CC=C(CCNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 1, 1, 1, 1, 1, 8, 17, 61, 61, 61, 77, 77, 77, 77, 77, 1, 1, 5, 5, 5, 1, 1, 1, 8, 8, 17, 17, 61, 77, 1, 1, 1, 1] 99 rigid atoms, others: [32, 1, 34, 3, 4, 5, 6, 7, 18, 19, 23, 24, 25, 33, 35] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 26, 27, 28, 29, 30, 31]) total number of confs: 230 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042253 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042253 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042253/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042253 Building REAL250005042254 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042254' /scratch/stefan/7921153/working/building/REAL250005042254 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042254 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042254/0 /scratch/stefan/7921153/working/building/REAL250005042254 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 363) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/363 `/scratch/stefan/7921153/working/3D/363' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CO)N1CC=C(CCNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005042254.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042254.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042254/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042254 none O=C(CO)N1CC=C(CCNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 8, 5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 546 conformations in input total number of sets (complete confs): 546 using faster count positions algorithm for large data unique positions, atoms: [175, 111, 175, 182, 111, 111, 111, 50, 27, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 111, 111, 182, 182, 546, 111, 111, 111, 50, 50, 27, 27, 5, 1, 111, 111, 111, 111] 546 rigid atoms, others: [32, 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, 33, 34, 35, 36]) total number of confs: 1108 number of broken/clashed sets: 75 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042254 none O=C(CO)N1CC=C(CCNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 8, 5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 546 conformations in input total number of sets (complete confs): 546 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 23, 1, 1, 1, 1, 1, 8, 16, 80, 80, 80, 111, 111, 111, 111, 111, 1, 1, 23, 23, 69, 1, 1, 1, 8, 8, 16, 16, 80, 111, 1, 1, 1, 1] 546 rigid atoms, others: [1, 34, 33, 4, 5, 6, 7, 8, 19, 20, 24, 25, 26, 36, 35] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 27, 28, 29, 30, 31, 32]) total number of confs: 432 number of broken/clashed sets: 75 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042254 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042254 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042254/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042254 Building REAL250005042255 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042255' /scratch/stefan/7921153/working/building/REAL250005042255 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042255 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042255/0 /scratch/stefan/7921153/working/building/REAL250005042255 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 364) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/364 `/scratch/stefan/7921153/working/3D/364' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(=O)N1CC=C(CCNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005042255.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042255.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042255/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042255 none C=CC(=O)N1CC=C(CCNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 11, 8, 5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 159 conformations in input total number of sets (complete confs): 159 using faster count positions algorithm for large data unique positions, atoms: [159, 159, 102, 159, 102, 102, 102, 45, 30, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 102, 102, 159, 159, 159, 102, 102, 102, 45, 45, 30, 30, 7, 1, 102, 102, 102, 102] 159 rigid atoms, others: [32, 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, 33, 34, 35, 36]) total number of confs: 457 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042255 none C=CC(=O)N1CC=C(CCNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 11, 8, 5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 159 conformations in input total number of sets (complete confs): 159 using faster count positions algorithm for large data unique positions, atoms: [33, 6, 1, 6, 1, 1, 1, 1, 1, 9, 18, 79, 79, 79, 102, 102, 102, 102, 102, 1, 1, 33, 33, 33, 1, 1, 1, 9, 9, 18, 18, 79, 102, 1, 1, 1, 1] 159 rigid atoms, others: [33, 2, 35, 4, 5, 6, 7, 8, 34, 19, 20, 24, 25, 26, 36] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 27, 28, 29, 30, 31, 32]) total number of confs: 350 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042255 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042255 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042255/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042255 Building REAL250005042256 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042256' /scratch/stefan/7921153/working/building/REAL250005042256 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042256 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042256/0 /scratch/stefan/7921153/working/building/REAL250005042256 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 365) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/365 `/scratch/stefan/7921153/working/3D/365' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)NCCC1(CNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005042256.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042256.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042256/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042256 none CCC(=O)NCCC1(CNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 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, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 145, 145, 145, 103, 77, 52, 17, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 52, 52, 201, 201, 201, 201, 201, 145, 103, 103, 77, 77, 17, 17, 3, 1, 52, 52, 52, 52] 201 rigid atoms, others: [33, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37]) total number of confs: 916 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042256 none CCC(=O)NCCC1(CNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 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, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 29, 29, 9, 5, 1, 1, 1, 10, 42, 42, 42, 52, 52, 52, 52, 52, 1, 1, 100, 100, 100, 100, 100, 29, 9, 9, 5, 5, 10, 10, 42, 52, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 6, 7, 8, 18, 19] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 502 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042256 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042256 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042256/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042256 Building REAL250005042257 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042257' /scratch/stefan/7921153/working/building/REAL250005042257 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042257 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042257/0 /scratch/stefan/7921153/working/building/REAL250005042257 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 366) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/366 `/scratch/stefan/7921153/working/3D/366' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCCC1(CNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005042257.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042257/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042257 none CC(=O)NCCC1(CNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 127, 82, 29, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 82, 82, 201, 201, 201, 201, 161, 161, 127, 127, 29, 29, 7, 1, 82, 82, 82, 82] 201 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34]) total number of confs: 818 number of broken/clashed sets: 13 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042257 none CC(=O)NCCC1(CNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 11, 7, 1, 1, 1, 10, 52, 52, 52, 82, 82, 82, 82, 82, 1, 1, 42, 42, 42, 42, 11, 11, 7, 7, 10, 10, 52, 82, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 5, 6, 7, 17, 18, 31] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 304 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042257 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042257 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042257/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042257 Building REAL250005042258 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042258' /scratch/stefan/7921153/working/building/REAL250005042258 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042258 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042258/0 /scratch/stefan/7921153/working/building/REAL250005042258 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 367) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/367 `/scratch/stefan/7921153/working/3D/367' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1(CCNC(=O)C2CC2)CC1)C1=CC(=O)[N-]O1) `REAL250005042258.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042258/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042258 none O=C(NCC1(CCNC(=O)C2CC2)CC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', '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', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 11, 32, 67, 80, 136, 136, 136, 201, 201, 32, 32, 1, 1, 1, 1, 1, 1, 3, 11, 11, 67, 67, 80, 80, 136, 201, 201, 201, 201, 201, 32, 32, 32, 32, 1] 201 rigid atoms, others: [1, 38, 15, 16, 17, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 759 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: REAL250005042258 none O=C(NCC1(CCNC(=O)C2CC2)CC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', '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', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 142, 107, 60, 44, 12, 12, 1, 12, 1, 1, 1, 107, 107, 201, 201, 201, 201, 201, 201, 201, 142, 142, 65, 65, 44, 44, 12, 1, 1, 1, 1, 1, 107, 107, 107, 107, 201] 201 rigid atoms, others: [32, 33, 8, 10, 11, 12, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36, 37, 38]) total number of confs: 800 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042258 none O=C(NCC1(CCNC(=O)C2CC2)CC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', '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', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 1, 1, 1, 7, 11, 44, 44, 44, 107, 107, 1, 1, 29, 32, 32, 32, 32, 32, 29, 8, 8, 7, 7, 11, 11, 44, 107, 107, 107, 107, 107, 1, 1, 1, 1, 32] 201 rigid atoms, others: [34, 3, 4, 5, 13, 14, 35, 36, 37] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38]) total number of confs: 386 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042258 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042258 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042258/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042258 Building REAL250005042259 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042259' /scratch/stefan/7921153/working/building/REAL250005042259 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042259 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042259/0 /scratch/stefan/7921153/working/building/REAL250005042259 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 368) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/368 `/scratch/stefan/7921153/working/3D/368' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)NCCC1(CNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005042259.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042259.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042259/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042259 none COCC(=O)NCCC1(CNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 128, 128, 128, 77, 62, 41, 15, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 41, 41, 201, 201, 201, 201, 201, 128, 77, 77, 62, 62, 15, 15, 3, 1, 41, 41, 41, 41] 201 rigid atoms, others: [34, 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, 35, 36, 37, 38]) total number of confs: 868 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042259 none COCC(=O)NCCC1(CNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 97, 24, 24, 24, 9, 5, 1, 1, 1, 10, 34, 34, 34, 41, 41, 41, 41, 41, 1, 1, 128, 128, 128, 97, 97, 24, 9, 9, 5, 5, 10, 10, 34, 41, 1, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 38, 7, 8, 9, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 512 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042259 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042259 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042259/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042259 Building REAL250005042260 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042260' /scratch/stefan/7921153/working/building/REAL250005042260 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042260 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042260/0 /scratch/stefan/7921153/working/building/REAL250005042260 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 369) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/369 `/scratch/stefan/7921153/working/3D/369' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(=O)NCCC1(CNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005042260.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042260/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042260 none CCCC(=O)NCCC1(CNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 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, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 198, 107, 107, 107, 72, 51, 37, 11, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 37, 37, 201, 201, 201, 201, 201, 198, 198, 107, 72, 72, 51, 51, 11, 11, 3, 1, 37, 37, 37, 37] 201 rigid atoms, others: [36, 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, 34, 35, 37, 38, 39, 40]) total number of confs: 909 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042260 none CCCC(=O)NCCC1(CNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 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, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 88, 19, 19, 19, 7, 4, 1, 1, 1, 10, 34, 34, 34, 37, 37, 37, 37, 37, 1, 1, 109, 109, 109, 109, 109, 88, 88, 19, 7, 7, 4, 4, 10, 10, 34, 37, 1, 1, 1, 1] 201 rigid atoms, others: [37, 38, 7, 8, 9, 39, 40, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 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]) total number of confs: 609 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042260 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042260 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042260/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042260 Building REAL250005042261 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042261' /scratch/stefan/7921153/working/building/REAL250005042261 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042261 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042261/0 /scratch/stefan/7921153/working/building/REAL250005042261 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 370) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/370 `/scratch/stefan/7921153/working/3D/370' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)NCCC1(CNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005042261.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042261.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042261/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042261 none CC(C)C(=O)NCCC1(CNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 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, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 161, 201, 161, 161, 108, 81, 50, 15, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 50, 50, 201, 201, 201, 201, 201, 201, 201, 161, 108, 108, 81, 81, 15, 15, 3, 1, 50, 50, 50, 50] 201 rigid atoms, others: [36, 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, 34, 35, 37, 38, 39, 40]) total number of confs: 886 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042261 none CC(C)C(=O)NCCC1(CNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 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, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 83, 29, 29, 9, 5, 1, 1, 1, 10, 43, 43, 43, 50, 50, 50, 50, 50, 1, 1, 83, 83, 83, 83, 83, 83, 83, 29, 9, 9, 5, 5, 10, 10, 43, 50, 1, 1, 1, 1] 201 rigid atoms, others: [37, 38, 7, 8, 9, 39, 40, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 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]) total number of confs: 445 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042261 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042261 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042261/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042261 Building REAL250005042262 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042262' /scratch/stefan/7921153/working/building/REAL250005042262 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042262 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042262/0 /scratch/stefan/7921153/working/building/REAL250005042262 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 371) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/371 `/scratch/stefan/7921153/working/3D/371' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C(=O)NCCC1(CNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005042262.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042262.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042262/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042262 none NC(=O)C(=O)NCCC1(CNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 6, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 191, 201, 191, 191, 115, 83, 55, 17, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 55, 55, 201, 201, 191, 115, 115, 83, 83, 17, 17, 3, 1, 55, 55, 55, 55] 201 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 31] 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, 32, 33, 34, 35]) total number of confs: 786 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042262 none NC(=O)C(=O)NCCC1(CNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 6, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 42, 72, 42, 42, 10, 6, 1, 1, 1, 10, 42, 42, 42, 55, 55, 55, 55, 55, 1, 1, 72, 72, 42, 10, 10, 6, 6, 10, 10, 42, 55, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 7, 8, 9, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 348 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042262 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042262 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042262/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042262 Building REAL250005042263 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042263' /scratch/stefan/7921153/working/building/REAL250005042263 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042263 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042263/0 /scratch/stefan/7921153/working/building/REAL250005042263 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 372) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/372 `/scratch/stefan/7921153/working/3D/372' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC(=O)NCCC1(CNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005042263.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042263.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042263/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042263 none C=CCC(=O)NCCC1(CNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 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, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 115, 115, 115, 78, 59, 41, 13, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 41, 41, 201, 201, 201, 201, 201, 115, 78, 78, 59, 59, 13, 13, 3, 1, 41, 41, 41, 41] 201 rigid atoms, others: [34, 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, 35, 36, 37, 38]) total number of confs: 886 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042263 none C=CCC(=O)NCCC1(CNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 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, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 94, 23, 23, 23, 8, 5, 1, 1, 1, 10, 34, 34, 34, 41, 41, 41, 41, 41, 1, 1, 130, 130, 130, 94, 94, 23, 8, 8, 5, 5, 10, 10, 34, 41, 1, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 38, 7, 8, 9, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 574 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042263 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042263 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042263/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042263 Building REAL250005042264 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042264' /scratch/stefan/7921153/working/building/REAL250005042264 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042264 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042264/0 /scratch/stefan/7921153/working/building/REAL250005042264 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 373) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/373 `/scratch/stefan/7921153/working/3D/373' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CO)NCCC1(CNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005042264.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042264.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042264/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042264 none O=C(CO)NCCC1(CNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 594 conformations in input total number of sets (complete confs): 594 using faster count positions algorithm for large data unique positions, atoms: [173, 173, 173, 198, 123, 97, 62, 19, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 62, 62, 198, 198, 594, 173, 123, 123, 97, 97, 19, 19, 3, 1, 62, 62, 62, 62] 594 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35]) total number of confs: 1431 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042264 none O=C(CO)NCCC1(CNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 594 conformations in input total number of sets (complete confs): 594 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 30, 128, 8, 5, 1, 1, 1, 10, 45, 45, 45, 62, 62, 62, 62, 62, 1, 1, 128, 128, 384, 30, 8, 8, 5, 5, 10, 10, 45, 62, 1, 1, 1, 1] 594 rigid atoms, others: [32, 33, 34, 35, 6, 7, 8, 18, 19] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 987 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042264 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042264 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042264/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042264 Building REAL250005042265 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042265' /scratch/stefan/7921153/working/building/REAL250005042265 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042265 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042265/0 /scratch/stefan/7921153/working/building/REAL250005042265 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 374) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/374 `/scratch/stefan/7921153/working/3D/374' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)C(=O)NCCC1(CNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005042265.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042265.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042265/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042265 none CC(O)C(=O)NCCC1(CNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [201, 149, 201, 149, 149, 101, 79, 51, 17, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 51, 51, 201, 201, 201, 201, 603, 149, 101, 101, 79, 79, 17, 17, 3, 1, 51, 51, 51, 51] 603 rigid atoms, others: [34, 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, 35, 36, 37, 38]) total number of confs: 1488 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042265 none CC(O)C(=O)NCCC1(CNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [117, 33, 117, 33, 33, 9, 5, 1, 1, 1, 10, 39, 39, 39, 51, 51, 51, 51, 51, 1, 1, 117, 117, 117, 117, 351, 33, 9, 9, 5, 5, 10, 10, 39, 51, 1, 1, 1, 1] 603 rigid atoms, others: [35, 36, 37, 38, 7, 8, 9, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 890 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042265 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042265 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042265/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042265 Building REAL250005042266 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042266' /scratch/stefan/7921153/working/building/REAL250005042266 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042266 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042266/0 /scratch/stefan/7921153/working/building/REAL250005042266 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 375) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/375 `/scratch/stefan/7921153/working/3D/375' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCF)NCCC1(CNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005042266.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042266.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042266/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042266 none O=C(CCF)NCCC1(CNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'F', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 15, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [119, 119, 119, 201, 201, 82, 61, 40, 11, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 40, 40, 201, 201, 201, 201, 119, 82, 82, 61, 61, 11, 11, 3, 1, 40, 40, 40, 40] 201 rigid atoms, others: [33, 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, 34, 35, 36, 37]) total number of confs: 855 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042266 none O=C(CCF)NCCC1(CNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'F', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 15, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 96, 119, 8, 5, 1, 1, 1, 10, 36, 36, 36, 40, 40, 40, 40, 40, 1, 1, 96, 96, 119, 119, 23, 8, 8, 5, 5, 10, 10, 36, 40, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 7, 8, 9, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 582 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042266 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042266 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042266/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042266 Building REAL250005042267 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042267' /scratch/stefan/7921153/working/building/REAL250005042267 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042267 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042267/0 /scratch/stefan/7921153/working/building/REAL250005042267 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 376) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/376 `/scratch/stefan/7921153/working/3D/376' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](O)C(=O)NCCC1(CNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005042267.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042267.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042267/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042267 none C[C@@H](O)C(=O)NCCC1(CNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [201, 151, 201, 201, 151, 151, 101, 79, 51, 17, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 51, 51, 201, 201, 201, 603, 151, 101, 101, 79, 79, 17, 17, 3, 1, 51, 51, 51, 51] 603 rigid atoms, others: [34, 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, 35, 36, 37, 38]) total number of confs: 1482 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042267 none C[C@@H](O)C(=O)NCCC1(CNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [119, 34, 119, 119, 34, 34, 9, 5, 1, 1, 1, 10, 40, 40, 40, 51, 51, 51, 51, 51, 1, 1, 119, 119, 119, 357, 34, 9, 9, 5, 5, 10, 10, 40, 51, 1, 1, 1, 1] 603 rigid atoms, others: [35, 36, 37, 38, 8, 9, 10, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 901 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042267 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042267 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042267/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042267 Building REAL250005042268 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042268' /scratch/stefan/7921153/working/building/REAL250005042268 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042268 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042268/0 /scratch/stefan/7921153/working/building/REAL250005042268 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 377) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/377 `/scratch/stefan/7921153/working/3D/377' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](O)C(=O)NCCC1(CNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005042268.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042268.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042268/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042268 none C[C@H](O)C(=O)NCCC1(CNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [201, 147, 201, 201, 147, 147, 100, 81, 53, 18, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 53, 53, 201, 201, 201, 603, 147, 100, 100, 81, 81, 18, 18, 3, 1, 53, 53, 53, 53] 603 rigid atoms, others: [34, 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, 35, 36, 37, 38]) total number of confs: 1485 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042268 none C[C@H](O)C(=O)NCCC1(CNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [116, 30, 116, 116, 30, 30, 9, 5, 1, 1, 1, 10, 40, 40, 40, 53, 53, 53, 53, 53, 1, 1, 116, 116, 116, 348, 30, 9, 9, 5, 5, 10, 10, 40, 53, 1, 1, 1, 1] 603 rigid atoms, others: [35, 36, 37, 38, 8, 9, 10, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 894 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042268 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042268 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042268/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042268 Building REAL250005042269 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042269' /scratch/stefan/7921153/working/building/REAL250005042269 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042269 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042269/0 /scratch/stefan/7921153/working/building/REAL250005042269 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 378) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/378 `/scratch/stefan/7921153/working/3D/378' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=CC(=O)NCCC1(CNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005042269.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042269.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042269/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042269 none CC=CC(=O)NCCC1(CNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 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, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 157, 157, 157, 107, 73, 56, 19, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 56, 56, 201, 201, 201, 201, 201, 157, 107, 107, 73, 73, 19, 19, 3, 1, 56, 56, 56, 56] 201 rigid atoms, others: [34, 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, 35, 36, 37, 38]) total number of confs: 800 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042269 none CC=CC(=O)NCCC1(CNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 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, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 37, 37, 37, 8, 5, 1, 1, 1, 10, 40, 40, 40, 56, 56, 56, 56, 56, 1, 1, 82, 82, 82, 82, 82, 37, 8, 8, 5, 5, 10, 10, 40, 56, 1, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 38, 7, 8, 9, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 377 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042269 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042269 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042269/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042269 Building REAL250005042270 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042270' /scratch/stefan/7921153/working/building/REAL250005042270 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042270 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042270/0 /scratch/stefan/7921153/working/building/REAL250005042270 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 379) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/379 `/scratch/stefan/7921153/working/3D/379' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)NCC1(CCNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005042270.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042270.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042270/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042270 none COCC(=O)NCC1(CCNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 177, 111, 111, 111, 69, 45, 27, 24, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 45, 45, 183, 183, 183, 177, 177, 111, 69, 69, 27, 27, 24, 24, 7, 1, 45, 45, 45, 45] 183 rigid atoms, others: [34, 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, 35, 36, 37, 38]) total number of confs: 759 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042270 none COCC(=O)NCC1(CCNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [151, 119, 30, 30, 30, 7, 1, 1, 1, 7, 9, 28, 28, 28, 45, 45, 45, 45, 45, 1, 1, 151, 151, 151, 119, 119, 30, 7, 7, 7, 7, 9, 9, 28, 45, 1, 1, 1, 1] 183 rigid atoms, others: [35, 36, 37, 6, 7, 8, 19, 20, 38] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 585 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042270 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042270 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042270/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042270 Building REAL250005042271 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042271' /scratch/stefan/7921153/working/building/REAL250005042271 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042271 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042271/0 /scratch/stefan/7921153/working/building/REAL250005042271 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 380) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/380 `/scratch/stefan/7921153/working/3D/380' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(=O)NCC1(CCNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005042271.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042271/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042271 none CCCC(=O)NCC1(CCNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 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, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 199, 120, 120, 120, 63, 33, 17, 11, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 33, 33, 201, 201, 201, 201, 201, 199, 199, 120, 63, 63, 18, 18, 11, 11, 3, 1, 33, 33, 33, 33] 201 rigid atoms, others: [36, 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, 34, 35, 37, 38, 39, 40]) total number of confs: 855 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042271 none CCCC(=O)NCC1(CCNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 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, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [119, 107, 23, 23, 23, 6, 1, 1, 1, 7, 10, 31, 31, 31, 33, 33, 33, 33, 33, 1, 1, 129, 129, 129, 129, 129, 107, 107, 23, 6, 6, 7, 7, 10, 10, 31, 33, 1, 1, 1, 1] 201 rigid atoms, others: [37, 6, 7, 8, 39, 40, 19, 20, 38] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 662 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042271 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042271 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042271/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042271 Building REAL250005042272 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042272' /scratch/stefan/7921153/working/building/REAL250005042272 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042272 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042272/0 /scratch/stefan/7921153/working/building/REAL250005042272 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 381) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/381 `/scratch/stefan/7921153/working/3D/381' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)NCC1(CCNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005042272.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042272/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042272 none CC(C)C(=O)NCC1(CCNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 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, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 166, 201, 166, 166, 105, 58, 25, 18, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 58, 58, 201, 201, 201, 201, 201, 201, 201, 166, 105, 105, 29, 29, 18, 18, 4, 1, 58, 58, 58, 58] 201 rigid atoms, others: [36, 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, 34, 35, 37, 38, 39, 40]) total number of confs: 836 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042272 none CC(C)C(=O)NCC1(CCNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 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, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 98, 30, 30, 9, 1, 1, 1, 7, 11, 49, 49, 49, 58, 58, 58, 58, 58, 1, 1, 98, 98, 98, 98, 98, 98, 98, 30, 9, 9, 7, 7, 11, 11, 49, 58, 1, 1, 1, 1] 201 rigid atoms, others: [37, 6, 7, 8, 39, 40, 19, 20, 38] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 505 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042272 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042272 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042272/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042272 Building REAL250005042273 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042273' /scratch/stefan/7921153/working/building/REAL250005042273 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042273 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042273/0 /scratch/stefan/7921153/working/building/REAL250005042273 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 382) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/382 `/scratch/stefan/7921153/working/3D/382' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)NCC1(CCNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005042273.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042273.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042273/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042273 none CCC(=O)NCC1(CCNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 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, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 152, 152, 152, 106, 63, 26, 19, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 63, 63, 201, 201, 201, 201, 201, 152, 106, 106, 30, 30, 19, 19, 4, 1, 63, 63, 63, 63] 201 rigid atoms, others: [33, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37]) total number of confs: 875 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042273 none CCC(=O)NCC1(CCNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 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, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 33, 33, 10, 1, 1, 1, 7, 12, 52, 52, 52, 63, 63, 63, 63, 63, 1, 1, 106, 106, 106, 106, 106, 33, 10, 10, 7, 7, 12, 12, 52, 63, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 5, 6, 7, 18, 19, 37] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 549 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042273 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042273 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042273/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042273 Building REAL250005042274 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042274' /scratch/stefan/7921153/working/building/REAL250005042274 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042274 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042274/0 /scratch/stefan/7921153/working/building/REAL250005042274 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 383) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/383 `/scratch/stefan/7921153/working/3D/383' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC1(CCNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005042274.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042274.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042274/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042274 none CC(=O)NCC1(CCNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 92, 42, 31, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 92, 92, 201, 201, 201, 201, 169, 169, 48, 48, 31, 31, 9, 1, 92, 92, 92, 92] 201 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34]) total number of confs: 801 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042274 none CC(=O)NCC1(CCNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 10, 1, 1, 1, 9, 17, 64, 64, 64, 92, 92, 92, 92, 92, 1, 1, 41, 41, 41, 41, 10, 10, 9, 9, 17, 17, 64, 92, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 4, 5, 6, 17, 18, 31] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 345 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042274 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042274 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042274/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042274 Building REAL250005042275 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042275' /scratch/stefan/7921153/working/building/REAL250005042275 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042275 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042275/0 /scratch/stefan/7921153/working/building/REAL250005042275 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 384) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/384 `/scratch/stefan/7921153/working/3D/384' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1(CNC(=O)C2CC2)CC1)C1=CC(=O)[N-]O1) `REAL250005042275.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042275/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042275 none O=C(NCCC1(CNC(=O)C2CC2)CC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', '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', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 12, 18, 35, 72, 127, 127, 127, 201, 201, 35, 35, 1, 1, 1, 1, 1, 1, 4, 12, 12, 21, 21, 72, 72, 127, 201, 201, 201, 201, 201, 35, 35, 35, 35, 1] 201 rigid atoms, others: [1, 38, 15, 16, 17, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 716 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: REAL250005042275 none O=C(NCCC1(CNC(=O)C2CC2)CC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', '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', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 147, 124, 102, 44, 10, 10, 1, 10, 1, 1, 1, 102, 102, 201, 201, 201, 201, 201, 201, 201, 147, 147, 124, 124, 44, 44, 10, 1, 1, 1, 1, 1, 102, 102, 102, 102, 201] 201 rigid atoms, others: [32, 33, 8, 10, 11, 12, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36, 37, 38]) total number of confs: 764 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042275 none O=C(NCCC1(CNC(=O)C2CC2)CC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', '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', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 5, 1, 1, 1, 10, 36, 36, 36, 103, 103, 1, 1, 33, 35, 35, 35, 35, 35, 33, 7, 7, 5, 5, 10, 10, 36, 103, 103, 103, 103, 103, 1, 1, 1, 1, 35] 201 rigid atoms, others: [34, 35, 4, 5, 6, 13, 14, 36, 37] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38]) total number of confs: 378 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042275 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042275 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042275/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042275 Building REAL250005042276 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042276' /scratch/stefan/7921153/working/building/REAL250005042276 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042276 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042276/0 /scratch/stefan/7921153/working/building/REAL250005042276 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 385) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/385 `/scratch/stefan/7921153/working/3D/385' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C(=O)NCC1(CCNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005042276.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042276/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042276 none NC(=O)C(=O)NCC1(CCNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 6, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 197, 201, 197, 197, 119, 58, 25, 18, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 58, 58, 201, 201, 197, 119, 119, 29, 29, 18, 18, 6, 1, 58, 58, 58, 58] 201 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 31] 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, 32, 33, 34, 35]) total number of confs: 740 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042276 none NC(=O)C(=O)NCC1(CCNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 6, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 77, 35, 35, 8, 1, 1, 1, 7, 13, 50, 50, 50, 58, 58, 58, 58, 58, 1, 1, 77, 77, 35, 8, 8, 7, 7, 13, 13, 50, 58, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 6, 7, 8, 19, 20] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 384 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042276 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042276 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042276/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042276 Building REAL250005042277 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042277' /scratch/stefan/7921153/working/building/REAL250005042277 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042277 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042277/0 /scratch/stefan/7921153/working/building/REAL250005042277 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 386) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/386 `/scratch/stefan/7921153/working/3D/386' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CO)NCC1(CCNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005042277.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042277/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042277 none O=C(CO)NCC1(CCNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 258 conformations in input total number of sets (complete confs): 258 using faster count positions algorithm for large data unique positions, atoms: [71, 71, 71, 86, 54, 38, 23, 20, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 38, 38, 86, 86, 258, 71, 54, 54, 23, 23, 20, 20, 8, 1, 38, 38, 38, 38] 258 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35]) total number of confs: 619 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042277 none O=C(CO)NCC1(CCNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 258 conformations in input total number of sets (complete confs): 258 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 28, 72, 7, 1, 1, 1, 7, 9, 26, 26, 26, 38, 38, 38, 38, 38, 1, 1, 72, 72, 216, 28, 7, 7, 7, 7, 9, 9, 26, 38, 1, 1, 1, 1] 258 rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 18, 19] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 570 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042277 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042277 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042277/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042277 Building REAL250005042278 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042278' /scratch/stefan/7921153/working/building/REAL250005042278 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042278 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042278/0 /scratch/stefan/7921153/working/building/REAL250005042278 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 387) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/387 `/scratch/stefan/7921153/working/3D/387' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)C(=O)NCC1(CCNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005042278.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042278/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042278 none CC(O)C(=O)NCC1(CCNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 291 conformations in input total number of sets (complete confs): 291 using faster count positions algorithm for large data unique positions, atoms: [97, 73, 97, 73, 73, 52, 36, 24, 21, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 36, 36, 97, 97, 97, 97, 291, 73, 52, 52, 24, 24, 21, 21, 6, 1, 36, 36, 36, 36] 291 rigid atoms, others: [34, 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, 35, 36, 37, 38]) total number of confs: 703 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042278 none CC(O)C(=O)NCC1(CCNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 291 conformations in input total number of sets (complete confs): 291 using faster count positions algorithm for large data unique positions, atoms: [69, 27, 69, 27, 27, 7, 1, 1, 1, 7, 9, 25, 25, 25, 36, 36, 36, 36, 36, 1, 1, 69, 69, 69, 69, 207, 27, 7, 7, 7, 7, 9, 9, 25, 36, 1, 1, 1, 1] 291 rigid atoms, others: [35, 36, 37, 6, 7, 8, 19, 20, 38] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 553 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042278 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042278 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042278/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042278 Building REAL250005042279 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042279' /scratch/stefan/7921153/working/building/REAL250005042279 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042279 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042279/0 /scratch/stefan/7921153/working/building/REAL250005042279 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 388) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/388 `/scratch/stefan/7921153/working/3D/388' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)C(=O)NCC1(CCNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005042279.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042279.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042279/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042279 none CC(=O)C(=O)NCC1(CCNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 191, 201, 191, 191, 124, 58, 23, 15, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 58, 58, 201, 201, 201, 191, 124, 124, 27, 27, 15, 15, 4, 1, 58, 58, 58, 58] 201 rigid atoms, others: [32, 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, 33, 34, 35, 36]) total number of confs: 757 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042279 none CC(=O)C(=O)NCC1(CCNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [75, 34, 75, 34, 34, 9, 1, 1, 1, 7, 14, 54, 54, 54, 58, 58, 58, 58, 58, 1, 1, 75, 75, 75, 34, 9, 9, 7, 7, 14, 14, 54, 58, 1, 1, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 6, 7, 8, 19, 20] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 388 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042279 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042279 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042279/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042279 Building REAL250005042280 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042280' /scratch/stefan/7921153/working/building/REAL250005042280 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042280 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042280/0 /scratch/stefan/7921153/working/building/REAL250005042280 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 389) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/389 `/scratch/stefan/7921153/working/3D/389' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=CC(=O)NCC1(CCNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005042280.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042280/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042280 none CC=CC(=O)NCC1(CCNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 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, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 156, 156, 156, 109, 65, 31, 24, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 65, 65, 201, 201, 201, 201, 201, 156, 109, 109, 34, 34, 24, 24, 6, 1, 65, 65, 65, 65] 201 rigid atoms, others: [34, 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, 35, 36, 37, 38]) total number of confs: 772 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042280 none CC=CC(=O)NCC1(CCNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 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, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 32, 32, 8, 1, 1, 1, 7, 11, 46, 46, 46, 65, 65, 65, 65, 65, 1, 1, 88, 88, 88, 88, 88, 32, 8, 8, 7, 7, 11, 11, 46, 65, 1, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 6, 7, 8, 19, 20, 38] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 416 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042280 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042280 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042280/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042280 Building REAL250005042281 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042281' /scratch/stefan/7921153/working/building/REAL250005042281 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042281 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042281/0 /scratch/stefan/7921153/working/building/REAL250005042281 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 390) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/390 `/scratch/stefan/7921153/working/3D/390' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](O)C(=O)NCC1(CCNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005042281.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042281.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042281/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042281 none C[C@H](O)C(=O)NCC1(CCNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 297 conformations in input total number of sets (complete confs): 297 using faster count positions algorithm for large data unique positions, atoms: [99, 73, 99, 99, 73, 73, 50, 34, 22, 20, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 34, 34, 99, 99, 99, 297, 73, 50, 50, 22, 22, 20, 20, 6, 1, 34, 34, 34, 34] 297 rigid atoms, others: [34, 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, 35, 36, 37, 38]) total number of confs: 712 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042281 none C[C@H](O)C(=O)NCC1(CCNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 297 conformations in input total number of sets (complete confs): 297 using faster count positions algorithm for large data unique positions, atoms: [75, 27, 75, 75, 27, 27, 7, 1, 1, 1, 7, 9, 24, 24, 24, 34, 34, 34, 34, 34, 1, 1, 75, 75, 75, 225, 27, 7, 7, 7, 7, 9, 9, 24, 34, 1, 1, 1, 1] 297 rigid atoms, others: [35, 36, 37, 38, 7, 8, 9, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 586 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042281 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042281 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042281/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042281 Building REAL250005042282 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042282' /scratch/stefan/7921153/working/building/REAL250005042282 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042282 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042282/0 /scratch/stefan/7921153/working/building/REAL250005042282 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 391) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/391 `/scratch/stefan/7921153/working/3D/391' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC(=O)NCC1(CCNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005042282.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042282.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042282/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042282 none C=CCC(=O)NCC1(CCNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 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, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 114, 114, 114, 70, 41, 19, 14, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 41, 41, 201, 201, 201, 201, 201, 114, 70, 70, 20, 20, 14, 14, 3, 1, 41, 41, 41, 41] 201 rigid atoms, others: [34, 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, 35, 36, 37, 38]) total number of confs: 855 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042282 none C=CCC(=O)NCC1(CCNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 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, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [127, 96, 24, 24, 24, 7, 1, 1, 1, 7, 10, 37, 37, 37, 41, 41, 41, 41, 41, 1, 1, 127, 127, 127, 96, 96, 24, 7, 7, 7, 7, 10, 10, 37, 41, 1, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 6, 7, 8, 19, 20, 38] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 573 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042282 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042282 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042282/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042282 Building REAL250005042283 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042283' /scratch/stefan/7921153/working/building/REAL250005042283 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042283 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042283/0 /scratch/stefan/7921153/working/building/REAL250005042283 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 392) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/392 `/scratch/stefan/7921153/working/3D/392' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CCC(=O)NCC1(CCNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005042283.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042283/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042283 none N#CCC(=O)NCC1(CCNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 154, 154, 154, 89, 48, 26, 22, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 48, 48, 201, 201, 154, 89, 89, 28, 28, 22, 22, 7, 1, 48, 48, 48, 48] 201 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 31] 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, 32, 33, 34, 35]) total number of confs: 818 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042283 none N#CCC(=O)NCC1(CCNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 26, 26, 7, 1, 1, 1, 7, 10, 37, 37, 37, 48, 48, 48, 48, 48, 1, 1, 114, 114, 26, 7, 7, 7, 7, 10, 10, 37, 48, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 6, 7, 8, 19, 20] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 528 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042283 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042283 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042283/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042283 Building REAL250005042284 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042284' /scratch/stefan/7921153/working/building/REAL250005042284 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042284 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042284/0 /scratch/stefan/7921153/working/building/REAL250005042284 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 393) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/393 `/scratch/stefan/7921153/working/3D/393' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCF)NCC1(CCNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005042284.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042284/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042284 none O=C(CCF)NCC1(CCNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'F', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 15, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [121, 121, 121, 201, 201, 74, 39, 17, 11, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 39, 39, 201, 201, 201, 201, 121, 74, 74, 19, 19, 11, 11, 3, 1, 39, 39, 39, 39] 201 rigid atoms, others: [33, 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, 34, 35, 36, 37]) total number of confs: 843 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042284 none O=C(CCF)NCC1(CCNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'F', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 15, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 106, 129, 7, 1, 1, 1, 7, 10, 37, 37, 37, 39, 39, 39, 39, 39, 1, 1, 106, 106, 129, 129, 25, 7, 7, 7, 7, 10, 10, 37, 39, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 6, 7, 8, 19, 20] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 607 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042284 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042284 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042284/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042284 Building REAL250005042285 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042285' /scratch/stefan/7921153/working/building/REAL250005042285 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042285 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042285/0 /scratch/stefan/7921153/working/building/REAL250005042285 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 394) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/394 `/scratch/stefan/7921153/working/3D/394' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](O)C(=O)NCC1(CCNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005042285.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042285/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042285 none C[C@@H](O)C(=O)NCC1(CCNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 291 conformations in input total number of sets (complete confs): 291 using faster count positions algorithm for large data unique positions, atoms: [97, 70, 97, 97, 70, 70, 49, 34, 23, 20, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 34, 34, 97, 97, 97, 291, 70, 49, 49, 23, 23, 20, 20, 6, 1, 34, 34, 34, 34] 291 rigid atoms, others: [34, 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, 35, 36, 37, 38]) total number of confs: 701 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042285 none C[C@@H](O)C(=O)NCC1(CCNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 291 conformations in input total number of sets (complete confs): 291 using faster count positions algorithm for large data unique positions, atoms: [72, 26, 72, 72, 26, 26, 7, 1, 1, 1, 7, 9, 24, 24, 24, 34, 34, 34, 34, 34, 1, 1, 72, 72, 72, 216, 26, 7, 7, 7, 7, 9, 9, 24, 34, 1, 1, 1, 1] 291 rigid atoms, others: [35, 36, 37, 38, 7, 8, 9, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 571 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042285 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042285 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042285/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042285 Building REAL250005042286 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042286' /scratch/stefan/7921153/working/building/REAL250005042286 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042286 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042286/0 /scratch/stefan/7921153/working/building/REAL250005042286 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 395) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/395 `/scratch/stefan/7921153/working/3D/395' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(=O)NCC1(CCNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005042286.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042286/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042286 none C=CC(=O)NCC1(CCNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 141, 77, 32, 23, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 77, 77, 201, 201, 201, 201, 141, 141, 37, 37, 23, 23, 4, 1, 77, 77, 77, 77] 201 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35]) total number of confs: 777 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042286 none C=CC(=O)NCC1(CCNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [92, 33, 33, 33, 8, 1, 1, 1, 7, 11, 53, 53, 53, 77, 77, 77, 77, 77, 1, 1, 92, 92, 92, 33, 8, 8, 7, 7, 11, 11, 53, 77, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 18, 19] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 451 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042286 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042286 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042286/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042286 Building REAL250005042287 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042287' /scratch/stefan/7921153/working/building/REAL250005042287 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042287 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042287/0 /scratch/stefan/7921153/working/building/REAL250005042287 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 396) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/396 `/scratch/stefan/7921153/working/3D/396' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)NC(C)CCCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005042287.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042287/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042287 none CCC(=O)NC(C)CCCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 135, 135, 135, 107, 45, 107, 48, 27, 17, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 135, 112, 112, 112, 107, 55, 55, 44, 48, 34, 34, 17, 17, 4, 1] 201 rigid atoms, others: [39, 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, 37, 38]) total number of confs: 1041 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042287 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042287 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042287/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042287 Building REAL250005042288 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042288' /scratch/stefan/7921153/working/building/REAL250005042288 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042288 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042288/0 /scratch/stefan/7921153/working/building/REAL250005042288 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 397) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/397 `/scratch/stefan/7921153/working/3D/397' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC(C)CCCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005042288.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042288/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042288 none CC(=O)NC(C)CCCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 163, 67, 157, 65, 38, 26, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 196, 196, 196, 196, 166, 167, 167, 160, 88, 88, 65, 63, 47, 47, 26, 26, 7, 1] 196 rigid atoms, others: [36, 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, 34, 35]) total number of confs: 975 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042288 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042288 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042288/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042288 Building REAL250005042289 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042289' /scratch/stefan/7921153/working/building/REAL250005042289 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042289 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042289/0 /scratch/stefan/7921153/working/building/REAL250005042289 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 398) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/398 `/scratch/stefan/7921153/working/3D/398' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCCCNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CC1) `REAL250005042289.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042289.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042289/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042289 none CC(CCCCNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 12, 26, 56, 64, 76, 112, 198, 199, 198, 200, 200, 200, 200, 200, 12, 1, 12, 1, 1, 1, 26, 26, 26, 26, 60, 60, 60, 64, 80, 80, 114, 113, 199, 200, 12, 1, 1, 1, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 40, 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]) total number of confs: 815 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042289 none CC(CCCCNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [92, 41, 41, 24, 17, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 91, 113, 113, 113, 200, 200, 92, 94, 94, 94, 47, 47, 41, 35, 31, 31, 17, 17, 4, 1, 113, 200, 200, 200, 200, 200] 201 rigid atoms, others: [34, 7, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40]) total number of confs: 831 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042289 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042289 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042289/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042289 Building REAL250005042290 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042290' /scratch/stefan/7921153/working/building/REAL250005042290 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042290 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042290/0 /scratch/stefan/7921153/working/building/REAL250005042290 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 399) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/399 `/scratch/stefan/7921153/working/3D/399' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)NC(C)CCCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005042290.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042290/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042290 none COCC(=O)NC(C)CCCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [193, 188, 106, 106, 107, 71, 37, 70, 39, 31, 23, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 193, 193, 193, 188, 188, 107, 72, 72, 72, 71, 41, 41, 39, 39, 35, 35, 23, 23, 5, 1] 196 rigid atoms, others: [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, 36, 37, 38, 39]) total number of confs: 890 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042290 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042290 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042290/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042290 Building REAL250005042291 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042291' /scratch/stefan/7921153/working/building/REAL250005042291 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042291 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042291/0 /scratch/stefan/7921153/working/building/REAL250005042291 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 400) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/400 `/scratch/stefan/7921153/working/3D/400' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(=O)NC(C)CCCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005042291.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042291.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042291/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042291 none CCCC(=O)NC(C)CCCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 189, 99, 99, 99, 78, 33, 79, 31, 22, 14, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 200, 200, 200, 199, 200, 190, 190, 99, 81, 81, 81, 80, 37, 37, 30, 31, 26, 26, 14, 14, 4, 1] 201 rigid atoms, others: [42, 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, 39, 40, 41]) total number of confs: 962 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042291 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042291 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042291/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042291 Building REAL250005042292 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042292' /scratch/stefan/7921153/working/building/REAL250005042292 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042292 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042292/0 /scratch/stefan/7921153/working/building/REAL250005042292 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 401) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/401 `/scratch/stefan/7921153/working/3D/401' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)NC(C)CCCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005042292.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042292/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042292 none CC(C)C(=O)NC(C)CCCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 147, 201, 147, 147, 107, 45, 110, 48, 25, 17, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 147, 114, 114, 114, 111, 56, 56, 41, 49, 33, 33, 17, 17, 4, 1] 201 rigid atoms, others: [42, 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, 39, 40, 41]) total number of confs: 1019 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042292 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042292 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042292/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042292 Building REAL250005042293 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042293' /scratch/stefan/7921153/working/building/REAL250005042293 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042293 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042293/0 /scratch/stefan/7921153/working/building/REAL250005042293 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 402) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/402 `/scratch/stefan/7921153/working/3D/402' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCCCNC(=O)C1=CC(=O)[N-]O1)NC(=O)C(N)=O) `REAL250005042293.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042293/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042293 none CC(CCCCNC(=O)C1=CC(=O)[N-]O1)NC(=O)C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [128, 53, 54, 28, 21, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 133, 196, 196, 196, 200, 200, 130, 134, 134, 132, 70, 70, 52, 50, 37, 37, 21, 21, 5, 1, 196, 200, 200] 201 rigid atoms, others: [34, 7, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37]) total number of confs: 945 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042293 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042293 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042293/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042293 Building REAL250005042294 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042294' /scratch/stefan/7921153/working/building/REAL250005042294 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042294 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042294/0 /scratch/stefan/7921153/working/building/REAL250005042294 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 403) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/403 `/scratch/stefan/7921153/working/3D/403' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC(=O)NC(C)CCCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005042294.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042294.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042294/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042294 none C=CCC(=O)NC(C)CCCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 200, 98, 98, 98, 78, 35, 76, 33, 22, 13, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 200, 200, 98, 79, 79, 79, 77, 39, 39, 32, 33, 26, 26, 13, 13, 4, 1] 201 rigid atoms, others: [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, 36, 37, 38, 39]) total number of confs: 959 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042294 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042294 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042294/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042294 Building REAL250005042295 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042295' /scratch/stefan/7921153/working/building/REAL250005042295 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042295 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042295/0 /scratch/stefan/7921153/working/building/REAL250005042295 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 404) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/404 `/scratch/stefan/7921153/working/3D/404' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCCCNC(=O)C1=CC(=O)[N-]O1)NC(=O)CO) `REAL250005042295.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042295/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042295 none CC(CCCCNC(=O)C1=CC(=O)[N-]O1)NC(=O)CO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 360 conformations in input total number of sets (complete confs): 360 using faster count positions algorithm for large data unique positions, atoms: [84, 39, 41, 28, 23, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 78, 95, 95, 95, 118, 84, 84, 84, 84, 46, 46, 35, 41, 35, 35, 23, 23, 6, 1, 95, 118, 118, 354] 360 rigid atoms, others: [33, 7, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37]) total number of confs: 959 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042295 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042295 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042295/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042295 Building REAL250005042296 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042296' /scratch/stefan/7921153/working/building/REAL250005042296 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042296 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042296/0 /scratch/stefan/7921153/working/building/REAL250005042296 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 405) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/405 `/scratch/stefan/7921153/working/3D/405' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)C(=O)NC(C)CCCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005042296.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042296.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042296/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042296 none CC(O)C(=O)NC(C)CCCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 474 conformations in input total number of sets (complete confs): 474 using faster count positions algorithm for large data unique positions, atoms: [154, 115, 155, 115, 116, 83, 40, 90, 44, 30, 26, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 155, 155, 155, 155, 465, 116, 90, 90, 90, 90, 50, 50, 38, 44, 38, 38, 26, 26, 7, 1] 474 rigid atoms, others: [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, 36, 37, 38, 39]) total number of confs: 1264 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042296 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042296 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042296/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042296 Building REAL250005042297 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042297' /scratch/stefan/7921153/working/building/REAL250005042297 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042297 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042297/0 /scratch/stefan/7921153/working/building/REAL250005042297 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 406) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/406 `/scratch/stefan/7921153/working/3D/406' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCCCNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@@H](C)O) `REAL250005042297.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042297/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042297 none CC(CCCCNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@@H](C)O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [73, 35, 39, 24, 19, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 65, 90, 90, 90, 132, 131, 132, 73, 73, 73, 73, 43, 43, 39, 32, 32, 32, 19, 19, 4, 1, 90, 131, 132, 132, 396] 402 rigid atoms, others: [35, 7, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 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: 1069 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042297 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042297 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042297/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042297 Building REAL250005042298 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042298' /scratch/stefan/7921153/working/building/REAL250005042298 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042298 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042298/0 /scratch/stefan/7921153/working/building/REAL250005042298 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 407) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/407 `/scratch/stefan/7921153/working/3D/407' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCCCNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@H](C)O) `REAL250005042298.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042298/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042298 none CC(CCCCNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@H](C)O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 477 conformations in input total number of sets (complete confs): 477 using faster count positions algorithm for large data unique positions, atoms: [90, 40, 44, 30, 26, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 83, 116, 117, 116, 156, 156, 156, 90, 90, 90, 90, 50, 50, 44, 38, 38, 38, 26, 26, 7, 1, 117, 156, 156, 156, 468] 477 rigid atoms, others: [35, 7, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 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: 1265 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042298 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042298 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042298/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042298 Building REAL250005042299 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042299' /scratch/stefan/7921153/working/building/REAL250005042299 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042299 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042299/0 /scratch/stefan/7921153/working/building/REAL250005042299 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 408) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/408 `/scratch/stefan/7921153/working/3D/408' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=CC(=O)NC(C)CCCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005042299.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042299.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042299/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042299 none CC=CC(=O)NC(C)CCCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 140, 140, 140, 119, 48, 118, 49, 28, 19, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 198, 198, 198, 198, 198, 140, 124, 124, 124, 119, 58, 58, 46, 50, 36, 36, 19, 19, 4, 1] 201 rigid atoms, others: [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, 36, 37, 38, 39]) total number of confs: 923 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042299 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042299 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042299/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042299 Building REAL250005042300 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042300' /scratch/stefan/7921153/working/building/REAL250005042300 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042300 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042300/0 /scratch/stefan/7921153/working/building/REAL250005042300 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 409) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/409 `/scratch/stefan/7921153/working/3D/409' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)NCCCCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005042300.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042300.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042300/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042300 none COCC(=O)NCCCCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 196, 103, 103, 103, 39, 22, 22, 19, 11, 4, 11, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 196, 196, 103, 39, 38, 23, 23, 21, 22, 20, 20, 11, 11, 11, 11, 4, 1] 201 rigid atoms, others: [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, 36, 37, 38, 39]) total number of confs: 830 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042300 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042300 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042300/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042300 Building REAL250005042301 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042301' /scratch/stefan/7921153/working/building/REAL250005042301 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042301 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042301/0 /scratch/stefan/7921153/working/building/REAL250005042301 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 410) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/410 `/scratch/stefan/7921153/working/3D/410' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(=O)NCCCCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005042301.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042301.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042301/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042301 none CCCC(=O)NCCCCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 191, 104, 104, 104, 49, 23, 22, 19, 9, 4, 9, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 191, 191, 104, 49, 49, 24, 24, 21, 22, 20, 20, 9, 9, 9, 9, 4, 1] 201 rigid atoms, others: [42, 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, 39, 40, 41]) total number of confs: 871 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042301 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042301 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042301/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042301 Building REAL250005042302 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042302' /scratch/stefan/7921153/working/building/REAL250005042302 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042302 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042302/0 /scratch/stefan/7921153/working/building/REAL250005042302 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 411) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/411 `/scratch/stefan/7921153/working/3D/411' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)NCCCCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005042302.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042302.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042302/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042302 none CC(C)C(=O)NCCCCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 155, 199, 155, 156, 74, 39, 34, 26, 9, 4, 9, 4, 1, 4, 1, 1, 1, 1, 1, 1, 200, 200, 198, 200, 200, 199, 200, 156, 74, 74, 40, 40, 33, 34, 27, 27, 9, 9, 9, 9, 4, 1] 201 rigid atoms, others: [42, 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, 39, 40, 41]) total number of confs: 869 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042302 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042302 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042302/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042302 Building REAL250005042303 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042303' /scratch/stefan/7921153/working/building/REAL250005042303 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042303 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042303/0 /scratch/stefan/7921153/working/building/REAL250005042303 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 412) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/412 `/scratch/stefan/7921153/working/3D/412' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)NCCCCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005042303.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042303/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042303 none CCC(=O)NCCCCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 148, 148, 148, 77, 41, 32, 24, 10, 4, 10, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 148, 77, 77, 42, 42, 31, 32, 25, 25, 10, 10, 10, 10, 4, 1] 201 rigid atoms, others: [39, 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, 37, 38]) total number of confs: 898 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042303 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042303 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042303/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042303 Building REAL250005042304 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042304' /scratch/stefan/7921153/working/building/REAL250005042304 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042304 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042304/0 /scratch/stefan/7921153/working/building/REAL250005042304 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 413) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/413 `/scratch/stefan/7921153/working/3D/413' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCCCCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005042304.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042304/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042304 none CC(=O)NCCCCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 83, 63, 51, 20, 8, 20, 8, 1, 8, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 144, 143, 86, 86, 62, 63, 53, 53, 20, 20, 20, 20, 8, 1] 201 rigid atoms, others: [36, 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, 34, 35]) total number of confs: 887 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042304 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042304 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042304/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042304 Building REAL250005042305 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042305' /scratch/stefan/7921153/working/building/REAL250005042305 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042305 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042305/0 /scratch/stefan/7921153/working/building/REAL250005042305 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 414) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/414 `/scratch/stefan/7921153/working/3D/414' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCCCNC(=O)C1CC1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005042305.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042305/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042305 none CC(CCCCNC(=O)C1CC1)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', '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.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 4, 9, 19, 22, 26, 55, 111, 111, 111, 201, 201, 4, 1, 4, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 20, 20, 22, 21, 27, 27, 55, 55, 111, 201, 201, 201, 201, 201, 4, 1] 201 rigid atoms, others: [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, 36, 37, 38, 39]) total number of confs: 717 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042305 none CC(CCCCNC(=O)C1CC1)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', '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.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 90, 88, 62, 46, 12, 12, 1, 12, 1, 1, 1, 162, 201, 201, 201, 201, 201, 201, 201, 201, 167, 167, 167, 166, 104, 104, 84, 86, 75, 75, 46, 46, 12, 1, 1, 1, 1, 1, 201, 201] 201 rigid atoms, others: [34, 35, 36, 37, 38, 7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40]) total number of confs: 1017 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042305 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042305 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042305/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042305 Building REAL250005042306 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042306' /scratch/stefan/7921153/working/building/REAL250005042306 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042306 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042306/0 /scratch/stefan/7921153/working/building/REAL250005042306 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 415) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/415 `/scratch/stefan/7921153/working/3D/415' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCCCNC(=O)C(N)=O)NC(=O)C1=CC(=O)[N-]O1) `REAL250005042306.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042306.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042306/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042306 none CC(CCCCNC(=O)C(N)=O)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.am', 'O.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 8, 11, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 6, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 12, 30, 38, 54, 94, 194, 195, 194, 201, 201, 4, 1, 4, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 31, 31, 37, 38, 56, 56, 94, 93, 195, 201, 201, 4, 1] 201 rigid atoms, others: [37, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 789 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042306 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042306 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042306/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042306 Building REAL250005042307 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042307' /scratch/stefan/7921153/working/building/REAL250005042307 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042307 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042307/0 /scratch/stefan/7921153/working/building/REAL250005042307 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 416) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/416 `/scratch/stefan/7921153/working/3D/416' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCCCNC(=O)CO)NC(=O)C1=CC(=O)[N-]O1) `REAL250005042307.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042307.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042307/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042307 none CC(CCCCNC(=O)CO)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [15, 6, 15, 39, 50, 65, 114, 198, 198, 198, 201, 6, 1, 6, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 42, 42, 49, 50, 69, 69, 115, 114, 198, 201, 201, 603, 6, 1] 603 rigid atoms, others: [37, 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: 1457 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042307 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042307 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042307/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042307 Building REAL250005042308 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042308' /scratch/stefan/7921153/working/building/REAL250005042308 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042308 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042308/0 /scratch/stefan/7921153/working/building/REAL250005042308 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 417) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/417 `/scratch/stefan/7921153/working/3D/417' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)C(=O)NCCCCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005042308.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042308.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042308/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042308 none CC(O)C(=O)NCCCCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [199, 147, 197, 147, 147, 63, 44, 39, 29, 14, 6, 14, 6, 1, 6, 1, 1, 1, 1, 1, 1, 199, 199, 199, 199, 597, 147, 65, 65, 46, 46, 37, 39, 31, 31, 14, 14, 14, 14, 6, 1] 603 rigid atoms, others: [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, 36, 37, 38, 39]) total number of confs: 1444 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042308 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042308 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042308/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042308 Building REAL250005042309 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042309' /scratch/stefan/7921153/working/building/REAL250005042309 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042309 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042309/0 /scratch/stefan/7921153/working/building/REAL250005042309 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 418) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/418 `/scratch/stefan/7921153/working/3D/418' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)C(=O)NCCCCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005042309.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042309/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042309 none CC(=O)C(=O)NCCCCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [200, 188, 200, 188, 188, 90, 48, 34, 27, 12, 4, 12, 4, 1, 4, 1, 1, 1, 1, 1, 1, 200, 200, 200, 188, 90, 89, 50, 50, 33, 34, 28, 28, 12, 12, 12, 12, 4, 1] 201 rigid atoms, others: [38, 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]) total number of confs: 776 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042309 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042309 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042309/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042309 Building REAL250005042310 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042310' /scratch/stefan/7921153/working/building/REAL250005042310 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042310 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042310/0 /scratch/stefan/7921153/working/building/REAL250005042310 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 419) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/419 `/scratch/stefan/7921153/working/3D/419' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=CC(=O)NCCCCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005042310.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042310/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042310 none CC=CC(=O)NCCCCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 154, 154, 154, 80, 41, 35, 29, 14, 5, 14, 5, 1, 5, 1, 1, 1, 1, 1, 1, 200, 200, 200, 200, 200, 154, 82, 82, 44, 44, 34, 35, 32, 32, 14, 14, 14, 14, 5, 1] 201 rigid atoms, others: [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, 36, 37, 38, 39]) total number of confs: 817 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042310 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042310 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042310/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042310 Building REAL250005042311 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042311' /scratch/stefan/7921153/working/building/REAL250005042311 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042311 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042311/0 /scratch/stefan/7921153/working/building/REAL250005042311 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 420) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/420 `/scratch/stefan/7921153/working/3D/420' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCCCNC(=O)[C@H](C)O)NC(=O)C1=CC(=O)[N-]O1) `REAL250005042311.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042311.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042311/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042311 none CC(CCCCNC(=O)[C@H](C)O)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 12, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [12, 5, 12, 32, 37, 49, 97, 186, 186, 186, 201, 201, 200, 5, 1, 5, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 33, 33, 36, 37, 50, 50, 97, 97, 186, 201, 201, 201, 603, 5, 1] 603 rigid atoms, others: [40, 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]) total number of confs: 1414 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042311 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042311 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042311/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042311 Building REAL250005042312 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042312' /scratch/stefan/7921153/working/building/REAL250005042312 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042312 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042312/0 /scratch/stefan/7921153/working/building/REAL250005042312 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 421) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/421 `/scratch/stefan/7921153/working/3D/421' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC(=O)NCCCCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005042312.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042312.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042312/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042312 none C=CCC(=O)NCCCCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 102, 102, 102, 43, 20, 19, 17, 8, 4, 8, 4, 1, 4, 1, 1, 1, 1, 1, 1, 200, 200, 200, 200, 200, 102, 43, 43, 21, 21, 18, 19, 18, 18, 8, 8, 8, 8, 4, 1] 201 rigid atoms, others: [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, 36, 37, 38, 39]) total number of confs: 825 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042312 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042312 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042312/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042312 Building REAL250005042313 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042313' /scratch/stefan/7921153/working/building/REAL250005042313 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042313 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042313/0 /scratch/stefan/7921153/working/building/REAL250005042313 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 422) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/422 `/scratch/stefan/7921153/working/3D/422' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCCCNC(=O)CC#N)NC(=O)C1=CC(=O)[N-]O1) `REAL250005042313.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042313.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042313/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042313 none CC(CCCCNC(=O)CC#N)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.1', 'N.1', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 1, 8, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 5, 12, 22, 28, 31, 58, 127, 127, 127, 201, 201, 5, 1, 5, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 24, 24, 26, 28, 33, 33, 59, 59, 127, 201, 201, 5, 1] 201 rigid atoms, others: [37, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 847 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042313 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042313 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042313/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042313 Building REAL250005042314 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042314' /scratch/stefan/7921153/working/building/REAL250005042314 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042314 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042314/0 /scratch/stefan/7921153/working/building/REAL250005042314 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 423) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/423 `/scratch/stefan/7921153/working/3D/423' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCCCNC(=O)[C@@H](C)O)NC(=O)C1=CC(=O)[N-]O1) `REAL250005042314.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042314.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042314/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042314 none CC(CCCCNC(=O)[C@@H](C)O)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 12, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [12, 4, 12, 32, 41, 52, 96, 183, 183, 183, 201, 201, 201, 4, 1, 4, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 34, 34, 41, 39, 54, 54, 97, 97, 183, 201, 201, 201, 603, 4, 1] 603 rigid atoms, others: [40, 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]) total number of confs: 1447 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042314 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042314 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042314/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042314 Building REAL250005042315 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042315' /scratch/stefan/7921153/working/building/REAL250005042315 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042315 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042315/0 /scratch/stefan/7921153/working/building/REAL250005042315 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 424) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/424 `/scratch/stefan/7921153/working/3D/424' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(=O)NCCCCC(C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005042315.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042315.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042315/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042315 none C=CC(=O)NCCCCC(C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 200, 200, 201, 111, 52, 38, 31, 11, 5, 11, 5, 1, 5, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 111, 111, 53, 53, 37, 38, 32, 32, 11, 11, 11, 11, 5, 1] 201 rigid atoms, others: [37, 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: 811 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042315 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042315 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042315/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042315 Building REAL250005042316 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042316' /scratch/stefan/7921153/working/building/REAL250005042316 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042316 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042316/0 /scratch/stefan/7921153/working/building/REAL250005042316 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 425) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/425 `/scratch/stefan/7921153/working/3D/425' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CC2CCC1C(CNC(=O)C1=CC(=O)[N-]O1)C2) `REAL250005042316.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042316.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042316/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042316 none CC(=O)N1CC2CCC1C(CNC(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [33, 32, 33, 32, 32, 32, 32, 32, 32, 19, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 32, 33, 33, 33, 32, 32, 32, 32, 32, 32, 32, 32, 32, 19, 19, 7, 1, 32, 32] 33 rigid atoms, others: [36, 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, 37, 38]) total number of confs: 111 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042316 none CC(=O)N1CC2CCC1C(CNC(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 25, 25, 25, 32, 32, 32, 32, 32, 1, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 25, 32, 1, 1] 33 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 9, 10, 38, 37, 20, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 33, 2, 34, 36, 35, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23]) total number of confs: 98 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042316 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042316 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042316/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042316 Building REAL250005042317 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042317' /scratch/stefan/7921153/working/building/REAL250005042317 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042317 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042317/0 /scratch/stefan/7921153/working/building/REAL250005042317 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 426) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/426 `/scratch/stefan/7921153/working/3D/426' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC1CC2CCC1N(C(=O)C1=CC(=O)[N-]O1)C2) `REAL250005042317.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042317/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042317 none CC(=O)NCC1CC2CCC1N(C(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 37, 24, 23, 24, 24, 24, 23, 23, 8, 1, 8, 1, 1, 1, 1, 1, 1, 24, 39, 39, 39, 39, 37, 37, 23, 24, 24, 24, 24, 24, 23, 24, 23, 1, 24, 24] 39 rigid atoms, others: [36, 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, 37, 38]) total number of confs: 115 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042317 none CC(=O)NCC1CC2CCC1N(C(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [17, 17, 17, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 23, 23, 23, 23, 23, 1, 17, 17, 17, 17, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 1, 1] 39 rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 11, 12, 38, 37, 20, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 36, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042317 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042317 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042317/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042317 Building REAL250005042318 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042318' /scratch/stefan/7921153/working/building/REAL250005042318 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042318 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042318/0 /scratch/stefan/7921153/working/building/REAL250005042318 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 427) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/427 `/scratch/stefan/7921153/working/3D/427' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N1CCC(CNC(=O)C2=CC(=O)[N-]O2)C(C)C1) `REAL250005042318.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042318/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042318 none CCC(=O)N1CCC(CNC(=O)C2=CC(=O)[N-]O2)C(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 36, 71, 36, 36, 36, 20, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 36, 36, 36, 71, 71, 71, 71, 71, 36, 36, 36, 36, 36, 19, 19, 5, 1, 36, 36, 36, 36, 36, 36] 71 rigid atoms, others: [34, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40]) total number of confs: 222 number of broken/clashed sets: 17 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042318 none CCC(=O)N1CCC(CNC(=O)C2=CC(=O)[N-]O2)C(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [16, 6, 1, 6, 1, 1, 1, 1, 1, 6, 29, 29, 29, 36, 36, 36, 36, 36, 1, 1, 1, 16, 16, 16, 16, 16, 1, 1, 1, 1, 1, 6, 6, 29, 36, 1, 2, 2, 2, 1, 1] 71 rigid atoms, others: [2, 35, 4, 5, 6, 7, 8, 39, 40, 18, 19, 20, 26, 27, 28, 29, 30] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 31, 32, 33, 34, 36, 37, 38]) total number of confs: 152 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042318 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042318 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042318/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042318 Building REAL250005042319 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042319' /scratch/stefan/7921153/working/building/REAL250005042319 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042319 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042319/0 /scratch/stefan/7921153/working/building/REAL250005042319 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 428) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/428 `/scratch/stefan/7921153/working/3D/428' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCC(CNC(=O)C2=CC(=O)[N-]O2)C(C)C1) `REAL250005042319.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042319.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042319/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042319 none CC(=O)N1CCC(CNC(=O)C2=CC(=O)[N-]O2)C(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [49, 41, 49, 41, 41, 41, 26, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 41, 41, 41, 49, 49, 49, 41, 41, 41, 41, 41, 25, 25, 6, 1, 41, 41, 41, 41, 41, 41] 49 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 31] 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, 32, 33, 34, 35, 36, 37]) total number of confs: 169 number of broken/clashed sets: 26 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042319 none CC(=O)N1CCC(CNC(=O)C2=CC(=O)[N-]O2)C(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 1, 1, 1, 1, 1, 7, 27, 27, 27, 41, 41, 41, 41, 41, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 27, 41, 1, 2, 2, 2, 1, 1] 49 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 17, 18, 19, 23, 24, 25, 26, 27, 37, 36] set([0, 33, 2, 34, 8, 9, 10, 11, 12, 13, 14, 15, 16, 35, 20, 21, 22, 28, 29, 30, 31]) total number of confs: 117 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042319 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042319 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042319/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042319 Building REAL250005042320 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042320' /scratch/stefan/7921153/working/building/REAL250005042320 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042320 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042320/0 /scratch/stefan/7921153/working/building/REAL250005042320 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 429) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/429 `/scratch/stefan/7921153/working/3D/429' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CN(C(=O)CO)CCC1CNC(=O)C1=CC(=O)[N-]O1) `REAL250005042320.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042320/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042320 none CC1CN(C(=O)CO)CCC1CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 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, 6, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 276 conformations in input total number of sets (complete confs): 276 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 53, 53, 53, 92, 92, 92, 53, 53, 26, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 53, 53, 53, 53, 53, 53, 92, 92, 276, 53, 53, 53, 53, 53, 25, 25, 5, 1] 276 rigid atoms, others: [38, 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]) total number of confs: 573 number of broken/clashed sets: 82 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042320 none CC1CN(C(=O)CO)CCC1CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 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, 6, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 276 conformations in input total number of sets (complete confs): 276 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 6, 6, 20, 1, 1, 1, 1, 7, 36, 36, 36, 53, 53, 53, 53, 53, 2, 2, 2, 1, 1, 1, 20, 20, 60, 1, 1, 1, 1, 1, 7, 7, 36, 53] 276 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 8, 9, 10, 11, 34, 24, 25, 26, 30, 31] set([5, 6, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 35, 36, 37, 38]) total number of confs: 261 number of broken/clashed sets: 82 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042320 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042320 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042320/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042320 Building REAL250005042321 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042321' /scratch/stefan/7921153/working/building/REAL250005042321 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042321 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042321/0 /scratch/stefan/7921153/working/building/REAL250005042321 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 430) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/430 `/scratch/stefan/7921153/working/3D/430' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)NCC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1C) `REAL250005042321.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042321/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042321 none CCC(=O)NCC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 159, 159, 159, 85, 36, 36, 36, 36, 11, 1, 11, 1, 1, 1, 1, 1, 1, 36, 36, 36, 201, 201, 201, 201, 201, 159, 85, 85, 36, 36, 36, 36, 36, 1, 36, 36, 36, 36, 36, 36] 201 rigid atoms, others: [34, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40]) total number of confs: 762 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042321 none CCC(=O)NCC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 30, 30, 6, 1, 1, 1, 1, 1, 1, 7, 7, 36, 36, 36, 36, 36, 1, 1, 1, 100, 100, 100, 100, 100, 30, 6, 6, 1, 1, 1, 1, 1, 36, 1, 1, 1, 2, 2, 2] 201 rigid atoms, others: [32, 33, 35, 36, 5, 6, 7, 8, 9, 10, 18, 19, 20, 37, 29, 30, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 34, 38, 39, 40]) total number of confs: 408 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042321 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042321 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042321/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042321 Building REAL250005042322 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042322' /scratch/stefan/7921153/working/building/REAL250005042322 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042322 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042322/0 /scratch/stefan/7921153/working/building/REAL250005042322 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 431) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/431 `/scratch/stefan/7921153/working/3D/431' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1C) `REAL250005042322.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042322/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042322 none CC(=O)NCC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 67, 36, 36, 36, 36, 11, 1, 11, 1, 1, 1, 1, 1, 1, 36, 36, 36, 91, 91, 91, 91, 67, 67, 36, 36, 36, 36, 36, 1, 36, 36, 36, 36, 36, 36] 91 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 31] 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, 32, 33, 34, 35, 36, 37]) total number of confs: 298 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042322 none CC(=O)NCC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [27, 27, 27, 8, 1, 1, 1, 1, 1, 1, 7, 7, 36, 36, 36, 36, 36, 1, 1, 1, 27, 27, 27, 27, 8, 8, 1, 1, 1, 1, 1, 36, 1, 1, 1, 2, 2, 2] 91 rigid atoms, others: [32, 33, 34, 4, 5, 6, 7, 8, 9, 17, 18, 19, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 36, 37, 10, 11, 12, 13, 14, 15, 16, 35, 20, 21, 22, 23, 24, 25, 31]) total number of confs: 130 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042322 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042322 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042322/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042322 Building REAL250005042323 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042323' /scratch/stefan/7921153/working/building/REAL250005042323 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042323 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042323/0 /scratch/stefan/7921153/working/building/REAL250005042323 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 432) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/432 `/scratch/stefan/7921153/working/3D/432' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CN(C(=O)C2=CC(=O)[N-]O2)CCC1CNC(=O)CO) `REAL250005042323.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042323.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042323/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042323 none CC1CN(C(=O)C2=CC(=O)[N-]O2)CCC1CNC(=O)CO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 357 conformations in input total number of sets (complete confs): 357 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 33, 11, 1, 11, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 71, 119, 119, 119, 118, 33, 33, 33, 33, 33, 33, 1, 33, 33, 33, 33, 33, 71, 71, 119, 119, 119, 357] 357 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 27] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 765 number of broken/clashed sets: 18 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042323 none CC1CN(C(=O)C2=CC(=O)[N-]O2)CCC1CNC(=O)CO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 357 conformations in input total number of sets (complete confs): 357 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 7, 7, 33, 33, 33, 33, 33, 1, 1, 1, 1, 7, 28, 28, 28, 52, 2, 2, 2, 1, 1, 1, 33, 1, 1, 1, 1, 1, 7, 7, 28, 53, 53, 159] 357 rigid atoms, others: [0, 1, 2, 3, 4, 32, 12, 13, 14, 15, 24, 25, 26, 28, 29, 30, 31] set([5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 27, 33, 34, 35, 36, 37, 38]) total number of confs: 404 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042323 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042323 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042323/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042323 Building REAL250005042324 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042324' /scratch/stefan/7921153/working/building/REAL250005042324 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042324 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042324/0 /scratch/stefan/7921153/working/building/REAL250005042324 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 433) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/433 `/scratch/stefan/7921153/working/3D/433' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(=O)NCC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1C) `REAL250005042324.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042324/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042324 none C=CC(=O)NCC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 151 conformations in input total number of sets (complete confs): 151 using faster count positions algorithm for large data unique positions, atoms: [151, 151, 151, 151, 76, 34, 34, 34, 34, 10, 1, 10, 1, 1, 1, 1, 1, 1, 34, 34, 34, 151, 151, 151, 151, 76, 76, 34, 34, 34, 34, 34, 1, 34, 34, 34, 34, 34, 34] 151 rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38]) total number of confs: 473 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042324 none C=CC(=O)NCC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [64, 29, 29, 29, 6, 1, 1, 1, 1, 1, 1, 7, 7, 34, 34, 34, 34, 34, 1, 1, 1, 64, 64, 64, 29, 6, 6, 1, 1, 1, 1, 1, 34, 1, 1, 1, 2, 2, 2] 151 rigid atoms, others: [33, 34, 35, 5, 6, 7, 8, 9, 10, 18, 19, 20, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 32, 36, 37, 38]) total number of confs: 234 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042324 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042324 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042324/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042324 Building REAL250005042325 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042325' /scratch/stefan/7921153/working/building/REAL250005042325 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042325 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042325/0 /scratch/stefan/7921153/working/building/REAL250005042325 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 434) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/434 `/scratch/stefan/7921153/working/3D/434' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N1CC[C@H]2CN(C(=O)C3=CC(=O)[N-]O3)C[C@H]21) `REAL250005042325.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042325/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042325 none CCC(=O)N1CC[C@H]2CN(C(=O)C3=CC(=O)[N-]O3)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [47, 39, 22, 39, 22, 22, 22, 22, 22, 22, 7, 1, 7, 1, 1, 1, 1, 1, 1, 22, 22, 22, 47, 47, 47, 47, 47, 22, 22, 22, 22, 22, 22, 1, 22, 22] 47 rigid atoms, others: [33, 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, 34, 35]) total number of confs: 143 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042325 none CCC(=O)N1CC[C@H]2CN(C(=O)C3=CC(=O)[N-]O3)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [13, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 22, 22, 22, 22, 22, 1, 1, 1, 14, 14, 14, 13, 13, 1, 1, 1, 1, 1, 1, 22, 1, 1] 47 rigid atoms, others: [32, 2, 35, 4, 5, 6, 7, 8, 9, 10, 11, 34, 19, 20, 21, 27, 28, 29, 30, 31] set([0, 1, 3, 33, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26]) total number of confs: 87 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042325 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042325 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042325/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042325 Building REAL250005042326 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042326' /scratch/stefan/7921153/working/building/REAL250005042326 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042326 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042326/0 /scratch/stefan/7921153/working/building/REAL250005042326 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 435) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/435 `/scratch/stefan/7921153/working/3D/435' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CC[C@H]2CN(C(=O)C3=CC(=O)[N-]O3)C[C@H]21) `REAL250005042326.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042326.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042326/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042326 none CC(=O)N1CC[C@H]2CN(C(=O)C3=CC(=O)[N-]O3)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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, 15, 24, 15, 15, 15, 15, 15, 14, 8, 1, 8, 1, 1, 1, 1, 1, 1, 15, 15, 15, 24, 24, 24, 15, 15, 15, 15, 14, 14, 1, 15, 15] 24 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32]) total number of confs: 67 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042326 none CC(=O)N1CC[C@H]2CN(C(=O)C3=CC(=O)[N-]O3)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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: [4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 14, 14, 14, 14, 14, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 15, 1, 1] 24 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 24, 25, 26, 27, 28, 29, 31] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 30]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042326 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042326 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042326/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042326 Building REAL250005042327 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042327' /scratch/stefan/7921153/working/building/REAL250005042327 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042327 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042327/0 /scratch/stefan/7921153/working/building/REAL250005042327 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 436) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/436 `/scratch/stefan/7921153/working/3D/436' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(C1=CC(=O)[N-]O1)N1C[C@@H]2CCN(C(=O)C3CC3)[C@@H]2C1) `REAL250005042327.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042327.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042327/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042327 none O=C(C1=CC(=O)[N-]O1)N1C[C@@H]2CCN(C(=O)C3CC3)[C@@H]2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [29, 9, 29, 34, 34, 34, 34, 34, 9, 9, 9, 9, 9, 9, 7, 1, 7, 1, 1, 1, 9, 9, 9, 34, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 9, 9] 34 rigid atoms, others: [32, 33, 34, 15, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36]) total number of confs: 82 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: REAL250005042327 none O=C(C1=CC(=O)[N-]O1)N1C[C@@H]2CCN(C(=O)C3CC3)[C@@H]2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 19, 20, 20, 20, 20, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 9, 9, 1, 1, 1, 19, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 1, 1] 35 rigid atoms, others: [1, 35, 36, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 24, 25, 26, 27, 28, 29] set([0, 32, 2, 3, 4, 5, 6, 7, 34, 16, 17, 18, 19, 23, 33, 30, 31]) total number of confs: 55 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042327 none O=C(C1=CC(=O)[N-]O1)N1C[C@@H]2CCN(C(=O)C3CC3)[C@@H]2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [8, 1, 1, 1, 1, 1, 1, 1, 8, 19, 19, 20, 19, 20, 20, 20, 29, 29, 35, 35, 20, 20, 20, 1, 19, 19, 19, 19, 20, 20, 35, 35, 35, 35, 35, 20, 20] 35 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 23] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042327 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042327 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042327/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042327 Building REAL250005042328 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042328' /scratch/stefan/7921153/working/building/REAL250005042328 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042328 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042328/0 /scratch/stefan/7921153/working/building/REAL250005042328 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 437) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/437 `/scratch/stefan/7921153/working/3D/437' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)N1CC[C@H]2CN(C(=O)C3=CC(=O)[N-]O3)C[C@H]21) `REAL250005042328.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042328.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042328/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042328 none COCC(=O)N1CC[C@H]2CN(C(=O)C3=CC(=O)[N-]O3)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 28, 19, 28, 19, 19, 19, 19, 19, 19, 7, 1, 7, 1, 1, 1, 1, 1, 1, 19, 19, 19, 42, 42, 42, 42, 42, 19, 19, 19, 19, 19, 19, 1, 19, 19] 42 rigid atoms, others: [34, 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, 35, 36]) total number of confs: 128 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042328 none COCC(=O)N1CC[C@H]2CN(C(=O)C3=CC(=O)[N-]O3)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [26, 15, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 19, 19, 19, 19, 19, 1, 1, 1, 26, 26, 26, 15, 15, 1, 1, 1, 1, 1, 1, 19, 1, 1] 42 rigid atoms, others: [32, 33, 3, 36, 5, 6, 7, 8, 9, 10, 11, 12, 35, 20, 21, 22, 28, 29, 30, 31] set([0, 1, 2, 34, 4, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27]) total number of confs: 100 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042328 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042328 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042328/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042328 Building REAL250005042329 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042329' /scratch/stefan/7921153/working/building/REAL250005042329 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042329 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042329/0 /scratch/stefan/7921153/working/building/REAL250005042329 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 438) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/438 `/scratch/stefan/7921153/working/3D/438' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(=O)N1CC[C@H]2CN(C(=O)C3=CC(=O)[N-]O3)C[C@H]21) `REAL250005042329.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042329/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042329 none CCCC(=O)N1CC[C@H]2CN(C(=O)C3=CC(=O)[N-]O3)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 84, 56, 30, 56, 30, 30, 30, 29, 29, 29, 9, 1, 9, 1, 1, 1, 1, 1, 1, 29, 29, 30, 85, 85, 85, 85, 85, 84, 84, 30, 30, 30, 30, 29, 29, 1, 29, 29] 85 rigid atoms, others: [36, 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, 37, 38]) total number of confs: 289 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042329 none CCCC(=O)N1CC[C@H]2CN(C(=O)C3=CC(=O)[N-]O3)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [26, 22, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 29, 29, 29, 29, 29, 1, 1, 1, 29, 29, 29, 29, 29, 22, 22, 1, 1, 1, 1, 1, 1, 29, 1, 1] 85 rigid atoms, others: [32, 33, 34, 3, 5, 6, 7, 8, 9, 10, 11, 12, 35, 20, 21, 22, 38, 37, 30, 31] set([0, 1, 2, 4, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 36]) total number of confs: 169 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042329 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042329 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042329/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042329 Building REAL250005042330 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042330' /scratch/stefan/7921153/working/building/REAL250005042330 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042330 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042330/0 /scratch/stefan/7921153/working/building/REAL250005042330 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 439) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/439 `/scratch/stefan/7921153/working/3D/439' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N1CC[C@H]2CN(C(=O)C3=CC(=O)[N-]O3)C[C@H]21) `REAL250005042330.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042330/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042330 none CC(C)C(=O)N1CC[C@H]2CN(C(=O)C3=CC(=O)[N-]O3)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 16, 25, 16, 16, 16, 15, 16, 15, 7, 1, 7, 1, 1, 1, 1, 1, 1, 16, 16, 16, 25, 25, 25, 25, 25, 25, 25, 16, 16, 16, 16, 15, 15, 1, 16, 16] 25 rigid atoms, others: [36, 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, 37, 38]) total number of confs: 62 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042330 none CC(C)C(=O)N1CC[C@H]2CN(C(=O)C3=CC(=O)[N-]O3)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [8, 5, 8, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 15, 15, 16, 16, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 15, 1, 1] 25 rigid atoms, others: [32, 33, 34, 3, 5, 6, 7, 8, 9, 10, 11, 12, 35, 20, 21, 22, 38, 37, 30, 31] set([0, 1, 2, 4, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 36]) total number of confs: 55 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042330 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042330 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042330/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042330 Building REAL250005042331 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042331' /scratch/stefan/7921153/working/building/REAL250005042331 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042331 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042331/0 /scratch/stefan/7921153/working/building/REAL250005042331 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 440) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/440 `/scratch/stefan/7921153/working/3D/440' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C(=O)N1CC[C@H]2CN(C(=O)C3=CC(=O)[N-]O3)C[C@H]21) `REAL250005042331.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042331.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042331/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042331 none NC(=O)C(=O)N1CC[C@H]2CN(C(=O)C3=CC(=O)[N-]O3)C[C@H]21 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [47, 35, 47, 22, 35, 22, 22, 22, 22, 22, 21, 8, 1, 8, 1, 1, 1, 1, 1, 1, 21, 22, 22, 47, 47, 22, 22, 22, 22, 21, 21, 1, 22, 21] 47 rigid atoms, others: [12, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33]) total number of confs: 138 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042331 none NC(=O)C(=O)N1CC[C@H]2CN(C(=O)C3=CC(=O)[N-]O3)C[C@H]21 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [14, 4, 14, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 21, 21, 21, 21, 21, 1, 1, 1, 15, 15, 1, 1, 1, 1, 1, 1, 21, 1, 1] 47 rigid atoms, others: [32, 33, 3, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 25, 26, 27, 28, 29, 30] set([0, 1, 2, 4, 13, 14, 15, 16, 17, 18, 19, 23, 24, 31]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042331 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042331 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042331/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042331 Building REAL250005042332 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042332' /scratch/stefan/7921153/working/building/REAL250005042332 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042332 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042332/0 /scratch/stefan/7921153/working/building/REAL250005042332 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 441) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/441 `/scratch/stefan/7921153/working/3D/441' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC(=O)N1CC[C@H]2CN(C(=O)C3=CC(=O)[N-]O3)C[C@H]21) `REAL250005042332.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042332.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042332/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042332 none C=CCC(=O)N1CC[C@H]2CN(C(=O)C3=CC(=O)[N-]O3)C[C@H]21 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 24, 16, 24, 16, 16, 16, 16, 16, 16, 7, 1, 7, 1, 1, 1, 1, 1, 1, 15, 16, 16, 47, 47, 47, 47, 47, 16, 16, 16, 16, 16, 16, 1, 15, 15] 47 rigid atoms, others: [34, 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, 35, 36]) total number of confs: 174 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042332 none C=CCC(=O)N1CC[C@H]2CN(C(=O)C3=CC(=O)[N-]O3)C[C@H]21 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [24, 17, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 16, 16, 16, 16, 15, 1, 1, 1, 24, 24, 24, 17, 17, 1, 1, 1, 1, 1, 1, 16, 1, 1] 47 rigid atoms, others: [32, 33, 3, 36, 5, 6, 7, 8, 9, 10, 11, 12, 35, 20, 21, 22, 28, 29, 30, 31] set([0, 1, 2, 34, 4, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042332 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042332 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042332/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042332 Building REAL250005042333 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042333' /scratch/stefan/7921153/working/building/REAL250005042333 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042333 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042333/0 /scratch/stefan/7921153/working/building/REAL250005042333 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 442) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/442 `/scratch/stefan/7921153/working/3D/442' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CO)N1CC[C@H]2CN(C(=O)C3=CC(=O)[N-]O3)C[C@H]21) `REAL250005042333.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042333.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042333/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042333 none O=C(CO)N1CC[C@H]2CN(C(=O)C3=CC(=O)[N-]O3)C[C@H]21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [28, 21, 28, 30, 21, 21, 21, 21, 21, 21, 7, 1, 7, 1, 1, 1, 1, 1, 1, 21, 21, 21, 30, 30, 90, 21, 21, 21, 21, 21, 21, 1, 21, 21] 90 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 31] 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, 32, 33]) total number of confs: 162 number of broken/clashed sets: 16 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042333 none O=C(CO)N1CC[C@H]2CN(C(=O)C3=CC(=O)[N-]O3)C[C@H]21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 14, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 21, 21, 21, 21, 21, 1, 1, 1, 14, 14, 42, 1, 1, 1, 1, 1, 1, 21, 1, 1] 90 rigid atoms, others: [32, 1, 33, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 25, 26, 27, 28, 29, 30] set([0, 2, 3, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 31]) total number of confs: 121 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042333 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042333 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042333/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042333 Building REAL250005042334 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042334' /scratch/stefan/7921153/working/building/REAL250005042334 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042334 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042334/0 /scratch/stefan/7921153/working/building/REAL250005042334 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 443) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/443 `/scratch/stefan/7921153/working/3D/443' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)C(=O)N1CC[C@H]2CN(C(=O)C3=CC(=O)[N-]O3)C[C@H]21) `REAL250005042334.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042334.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042334/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042334 none CC(O)C(=O)N1CC[C@H]2CN(C(=O)C3=CC(=O)[N-]O3)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [23, 20, 23, 14, 20, 14, 14, 14, 14, 14, 14, 7, 1, 7, 1, 1, 1, 1, 1, 1, 14, 14, 14, 23, 23, 23, 23, 69, 14, 14, 14, 14, 14, 14, 1, 14, 14] 69 rigid atoms, others: [34, 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, 35, 36]) total number of confs: 130 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042334 none CC(O)C(=O)N1CC[C@H]2CN(C(=O)C3=CC(=O)[N-]O3)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [11, 4, 11, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 14, 14, 14, 14, 14, 1, 1, 1, 11, 11, 11, 11, 33, 1, 1, 1, 1, 1, 1, 14, 1, 1] 69 rigid atoms, others: [32, 33, 3, 36, 5, 6, 7, 8, 9, 10, 11, 12, 35, 20, 21, 22, 28, 29, 30, 31] set([0, 1, 2, 34, 4, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27]) total number of confs: 93 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042334 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042334 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042334/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042334 Building REAL250005042335 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042335' /scratch/stefan/7921153/working/building/REAL250005042335 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042335 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042335/0 /scratch/stefan/7921153/working/building/REAL250005042335 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 444) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/444 `/scratch/stefan/7921153/working/3D/444' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCF)N1CC[C@H]2CN(C(=O)C3=CC(=O)[N-]O3)C[C@H]21) `REAL250005042335.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042335.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042335/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042335 none O=C(CCF)N1CC[C@H]2CN(C(=O)C3=CC(=O)[N-]O3)C[C@H]21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'F', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 15, 8, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [26, 21, 26, 42, 42, 21, 21, 21, 21, 21, 20, 6, 1, 6, 1, 1, 1, 1, 1, 1, 20, 21, 21, 42, 42, 42, 42, 21, 21, 21, 21, 20, 20, 1, 21, 21] 42 rigid atoms, others: [33, 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, 34, 35]) total number of confs: 134 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042335 none O=C(CCF)N1CC[C@H]2CN(C(=O)C3=CC(=O)[N-]O3)C[C@H]21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'F', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 15, 8, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 10, 20, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 20, 20, 20, 20, 20, 1, 1, 1, 10, 10, 20, 20, 1, 1, 1, 1, 1, 1, 20, 1, 1] 42 rigid atoms, others: [32, 1, 34, 35, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 27, 28, 29, 30, 31] set([0, 33, 2, 3, 4, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042335 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042335 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042335/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042335 Building REAL250005042336 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042336' /scratch/stefan/7921153/working/building/REAL250005042336 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042336 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042336/0 /scratch/stefan/7921153/working/building/REAL250005042336 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 445) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/445 `/scratch/stefan/7921153/working/3D/445' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](O)C(=O)N1CC[C@H]2CN(C(=O)C3=CC(=O)[N-]O3)C[C@H]21) `REAL250005042336.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042336.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042336/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042336 none C[C@@H](O)C(=O)N1CC[C@H]2CN(C(=O)C3=CC(=O)[N-]O3)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [48, 40, 48, 48, 22, 40, 22, 22, 22, 22, 22, 22, 9, 1, 9, 1, 1, 1, 1, 1, 1, 22, 22, 22, 48, 48, 48, 144, 22, 22, 22, 22, 22, 22, 1, 22, 22] 144 rigid atoms, others: [34, 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, 35, 36]) total number of confs: 291 number of broken/clashed sets: 25 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042336 none C[C@@H](O)C(=O)N1CC[C@H]2CN(C(=O)C3=CC(=O)[N-]O3)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [15, 4, 15, 15, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 22, 22, 22, 22, 22, 1, 1, 1, 15, 15, 15, 45, 1, 1, 1, 1, 1, 1, 22, 1, 1] 144 rigid atoms, others: [32, 33, 35, 4, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 36, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 34, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27]) total number of confs: 130 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042336 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042336 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042336/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042336 Building REAL250005042337 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042337' /scratch/stefan/7921153/working/building/REAL250005042337 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042337 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042337/0 /scratch/stefan/7921153/working/building/REAL250005042337 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 446) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/446 `/scratch/stefan/7921153/working/3D/446' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](O)C(=O)N1CC[C@H]2CN(C(=O)C3=CC(=O)[N-]O3)C[C@H]21) `REAL250005042337.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042337.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042337/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042337 none C[C@H](O)C(=O)N1CC[C@H]2CN(C(=O)C3=CC(=O)[N-]O3)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [30, 20, 30, 30, 18, 20, 18, 18, 18, 18, 18, 18, 7, 1, 7, 1, 1, 1, 1, 1, 1, 18, 18, 18, 30, 30, 30, 90, 18, 18, 18, 18, 18, 18, 1, 18, 18] 90 rigid atoms, others: [34, 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, 35, 36]) total number of confs: 177 number of broken/clashed sets: 16 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042337 none C[C@H](O)C(=O)N1CC[C@H]2CN(C(=O)C3=CC(=O)[N-]O3)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [9, 4, 9, 9, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 18, 18, 18, 18, 18, 1, 1, 1, 9, 9, 9, 27, 1, 1, 1, 1, 1, 1, 18, 1, 1] 90 rigid atoms, others: [32, 33, 35, 4, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 36, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 34, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27]) total number of confs: 84 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042337 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042337 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042337/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042337 Building REAL250005042338 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042338' /scratch/stefan/7921153/working/building/REAL250005042338 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042338 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042338/0 /scratch/stefan/7921153/working/building/REAL250005042338 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 447) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/447 `/scratch/stefan/7921153/working/3D/447' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=CC(=O)N1CC[C@H]2CN(C(=O)C3=CC(=O)[N-]O3)C[C@H]21) `REAL250005042338.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042338.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042338/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042338 none CC=CC(=O)N1CC[C@H]2CN(C(=O)C3=CC(=O)[N-]O3)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 50, 25, 50, 25, 25, 25, 25, 25, 25, 8, 1, 8, 1, 1, 1, 1, 1, 1, 25, 25, 25, 55, 55, 55, 55, 55, 25, 25, 25, 25, 25, 25, 1, 25, 25] 55 rigid atoms, others: [34, 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, 35, 36]) total number of confs: 141 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042338 none CC=CC(=O)N1CC[C@H]2CN(C(=O)C3=CC(=O)[N-]O3)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [16, 16, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 25, 25, 25, 25, 25, 1, 1, 1, 16, 16, 16, 16, 16, 1, 1, 1, 1, 1, 1, 25, 1, 1] 55 rigid atoms, others: [32, 33, 3, 36, 5, 6, 7, 8, 9, 10, 11, 12, 35, 20, 21, 22, 28, 29, 30, 31] set([0, 1, 2, 34, 4, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042338 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042338 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042338/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042338 Building REAL250005042339 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042339' /scratch/stefan/7921153/working/building/REAL250005042339 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042339 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042339/0 /scratch/stefan/7921153/working/building/REAL250005042339 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 448) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/448 `/scratch/stefan/7921153/working/3D/448' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)N1C[C@@H]2CCN(C(=O)C3=CC(=O)[N-]O3)[C@@H]2C1) `REAL250005042339.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042339/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042339 none COCC(=O)N1C[C@@H]2CCN(C(=O)C3=CC(=O)[N-]O3)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 29, 18, 29, 18, 18, 18, 18, 18, 18, 8, 1, 8, 1, 1, 1, 1, 1, 1, 18, 18, 18, 59, 59, 59, 59, 59, 18, 18, 18, 18, 18, 18, 1, 18, 18] 59 rigid atoms, others: [34, 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, 35, 36]) total number of confs: 203 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042339 none COCC(=O)N1C[C@@H]2CCN(C(=O)C3=CC(=O)[N-]O3)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 12, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 6, 18, 18, 18, 18, 18, 1, 1, 1, 29, 29, 29, 13, 13, 1, 1, 1, 1, 1, 1, 18, 1, 1] 59 rigid atoms, others: [32, 33, 3, 36, 5, 6, 7, 8, 9, 10, 11, 12, 35, 20, 21, 22, 28, 29, 30, 31] set([0, 1, 2, 34, 4, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042339 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042339 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042339/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042339 Building REAL250005042340 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042340' /scratch/stefan/7921153/working/building/REAL250005042340 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042340 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042340/0 /scratch/stefan/7921153/working/building/REAL250005042340 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 449) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/449 `/scratch/stefan/7921153/working/3D/449' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(=O)N1C[C@@H]2CCN(C(=O)C3=CC(=O)[N-]O3)[C@@H]2C1) `REAL250005042340.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042340.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042340/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042340 none CCCC(=O)N1C[C@@H]2CCN(C(=O)C3=CC(=O)[N-]O3)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 39, 22, 39, 22, 22, 22, 22, 22, 22, 8, 1, 8, 1, 1, 1, 1, 1, 1, 21, 22, 22, 74, 74, 74, 74, 74, 74, 74, 22, 22, 22, 22, 22, 22, 1, 22, 22] 74 rigid atoms, others: [36, 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, 37, 38]) total number of confs: 269 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042340 none CCCC(=O)N1C[C@@H]2CCN(C(=O)C3=CC(=O)[N-]O3)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [24, 17, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 22, 22, 22, 22, 22, 1, 1, 1, 26, 26, 26, 25, 25, 17, 17, 1, 1, 1, 1, 1, 1, 22, 1, 1] 74 rigid atoms, others: [32, 33, 34, 3, 5, 6, 7, 8, 9, 10, 11, 12, 35, 20, 21, 22, 38, 37, 30, 31] set([0, 1, 2, 4, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 36]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042340 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042340 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042340/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042340 Building REAL250005042341 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042341' /scratch/stefan/7921153/working/building/REAL250005042341 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042341 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042341/0 /scratch/stefan/7921153/working/building/REAL250005042341 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 450) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/450 `/scratch/stefan/7921153/working/3D/450' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N1C[C@@H]2CCN(C(=O)C3=CC(=O)[N-]O3)[C@@H]2C1) `REAL250005042341.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042341/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042341 none CC(C)C(=O)N1C[C@@H]2CCN(C(=O)C3=CC(=O)[N-]O3)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 14, 30, 14, 14, 14, 14, 14, 14, 7, 1, 7, 1, 1, 1, 1, 1, 1, 14, 14, 14, 30, 30, 30, 30, 30, 30, 30, 14, 14, 14, 14, 14, 14, 1, 14, 14] 30 rigid atoms, others: [36, 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, 37, 38]) total number of confs: 71 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042341 none CC(C)C(=O)N1C[C@@H]2CCN(C(=O)C3=CC(=O)[N-]O3)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [11, 7, 11, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 14, 14, 14, 14, 14, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 14, 1, 1] 30 rigid atoms, others: [32, 33, 34, 3, 5, 6, 7, 8, 9, 10, 11, 12, 35, 20, 21, 22, 38, 37, 30, 31] set([0, 1, 2, 4, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 36]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042341 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042341 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042341/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042341 Building REAL250005042342 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042342' /scratch/stefan/7921153/working/building/REAL250005042342 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042342 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042342/0 /scratch/stefan/7921153/working/building/REAL250005042342 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 451) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/451 `/scratch/stefan/7921153/working/3D/451' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N1C[C@@H]2CCN(C(=O)C3=CC(=O)[N-]O3)[C@@H]2C1) `REAL250005042342.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042342/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042342 none CCC(=O)N1C[C@@H]2CCN(C(=O)C3=CC(=O)[N-]O3)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [27, 23, 13, 23, 13, 13, 13, 13, 13, 13, 8, 1, 8, 1, 1, 1, 1, 1, 1, 13, 13, 13, 27, 27, 27, 27, 27, 13, 13, 13, 13, 13, 13, 1, 13, 13] 27 rigid atoms, others: [33, 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, 34, 35]) total number of confs: 77 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042342 none CCC(=O)N1C[C@@H]2CCN(C(=O)C3=CC(=O)[N-]O3)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [11, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 6, 7, 13, 13, 13, 13, 13, 1, 1, 1, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 13, 1, 1] 27 rigid atoms, others: [32, 2, 35, 4, 5, 6, 7, 8, 9, 10, 11, 34, 19, 20, 21, 27, 28, 29, 30, 31] set([0, 1, 3, 33, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042342 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042342 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042342/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042342 Building REAL250005042343 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042343' /scratch/stefan/7921153/working/building/REAL250005042343 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042343 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042343/0 /scratch/stefan/7921153/working/building/REAL250005042343 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 452) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/452 `/scratch/stefan/7921153/working/3D/452' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1C[C@@H]2CCN(C(=O)C3=CC(=O)[N-]O3)[C@@H]2C1) `REAL250005042343.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042343.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042343/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042343 none CC(=O)N1C[C@@H]2CCN(C(=O)C3=CC(=O)[N-]O3)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [13, 9, 13, 9, 9, 9, 9, 9, 9, 6, 1, 6, 1, 1, 1, 1, 1, 1, 9, 9, 9, 13, 13, 13, 9, 9, 9, 9, 9, 9, 1, 9, 9] 13 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32]) total number of confs: 35 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042343 none CC(=O)N1C[C@@H]2CCN(C(=O)C3=CC(=O)[N-]O3)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 9, 9, 9, 9, 9, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 1, 9, 1, 1] 13 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 24, 25, 26, 27, 28, 29, 31] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 30]) total number of confs: 25 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042343 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042343 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042343/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042343 Building REAL250005042344 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042344' /scratch/stefan/7921153/working/building/REAL250005042344 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042344 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042344/0 /scratch/stefan/7921153/working/building/REAL250005042344 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 453) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/453 `/scratch/stefan/7921153/working/3D/453' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(C1=CC(=O)[N-]O1)N1CC[C@H]2CN(C(=O)C3CC3)C[C@H]21) `REAL250005042344.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042344.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042344/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042344 none O=C(C1=CC(=O)[N-]O1)N1CC[C@H]2CN(C(=O)C3CC3)C[C@H]21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [26, 10, 26, 32, 32, 32, 32, 32, 10, 10, 10, 10, 10, 10, 7, 1, 7, 1, 1, 1, 10, 10, 10, 32, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 10, 10] 32 rigid atoms, others: [32, 33, 34, 15, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36]) total number of confs: 78 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: REAL250005042344 none O=C(C1=CC(=O)[N-]O1)N1CC[C@H]2CN(C(=O)C3CC3)C[C@H]21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 16, 16, 16, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 10, 10, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 1, 1] 32 rigid atoms, others: [1, 35, 36, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 24, 25, 26, 27, 28, 29] set([0, 32, 2, 3, 4, 5, 6, 7, 34, 16, 17, 18, 19, 23, 33, 30, 31]) total number of confs: 51 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042344 none O=C(C1=CC(=O)[N-]O1)N1CC[C@H]2CN(C(=O)C3CC3)C[C@H]21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [8, 1, 1, 1, 1, 1, 1, 1, 8, 16, 16, 16, 16, 16, 16, 16, 24, 24, 32, 32, 16, 16, 16, 1, 16, 16, 16, 16, 16, 16, 32, 32, 32, 32, 32, 16, 16] 32 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 23] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042344 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042344 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042344/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042344 Building REAL250005042345 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042345' /scratch/stefan/7921153/working/building/REAL250005042345 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042345 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042345/0 /scratch/stefan/7921153/working/building/REAL250005042345 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 454) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/454 `/scratch/stefan/7921153/working/3D/454' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C(=O)N1C[C@@H]2CCN(C(=O)C3=CC(=O)[N-]O3)[C@@H]2C1) `REAL250005042345.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042345.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042345/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042345 none NC(=O)C(=O)N1C[C@@H]2CCN(C(=O)C3=CC(=O)[N-]O3)[C@@H]2C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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, 29, 38, 19, 29, 19, 19, 19, 19, 19, 19, 9, 1, 9, 1, 1, 1, 1, 1, 1, 18, 19, 19, 38, 38, 19, 19, 19, 19, 19, 19, 1, 19, 19] 38 rigid atoms, others: [12, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33]) total number of confs: 112 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042345 none NC(=O)C(=O)N1C[C@@H]2CCN(C(=O)C3=CC(=O)[N-]O3)[C@@H]2C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [16, 5, 17, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 19, 19, 19, 19, 19, 1, 1, 1, 17, 17, 1, 1, 1, 1, 1, 1, 19, 1, 1] 38 rigid atoms, others: [32, 33, 3, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 25, 26, 27, 28, 29, 30] set([0, 1, 2, 4, 13, 14, 15, 16, 17, 18, 19, 23, 24, 31]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042345 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042345 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042345/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042345 Building REAL250005042346 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042346' /scratch/stefan/7921153/working/building/REAL250005042346 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042346 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042346/0 /scratch/stefan/7921153/working/building/REAL250005042346 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 455) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/455 `/scratch/stefan/7921153/working/3D/455' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CO)N1C[C@@H]2CCN(C(=O)C3=CC(=O)[N-]O3)[C@@H]2C1) `REAL250005042346.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042346/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042346 none O=C(CO)N1C[C@@H]2CCN(C(=O)C3=CC(=O)[N-]O3)[C@@H]2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 96 conformations in input total number of sets (complete confs): 96 using faster count positions algorithm for large data unique positions, atoms: [26, 18, 26, 32, 18, 18, 18, 18, 18, 18, 8, 1, 8, 1, 1, 1, 1, 1, 1, 18, 18, 18, 32, 32, 96, 18, 18, 18, 18, 18, 18, 1, 18, 18] 96 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 31] 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, 32, 33]) total number of confs: 195 number of broken/clashed sets: 13 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042346 none O=C(CO)N1C[C@@H]2CCN(C(=O)C3=CC(=O)[N-]O3)[C@@H]2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 96 conformations in input total number of sets (complete confs): 96 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 16, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 18, 18, 18, 18, 18, 1, 1, 1, 16, 16, 48, 1, 1, 1, 1, 1, 1, 18, 1, 1] 96 rigid atoms, others: [32, 1, 33, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 25, 26, 27, 28, 29, 30] set([0, 2, 3, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 31]) total number of confs: 127 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042346 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042346 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042346/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042346 Building REAL250005042347 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042347' /scratch/stefan/7921153/working/building/REAL250005042347 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042347 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042347/0 /scratch/stefan/7921153/working/building/REAL250005042347 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 456) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/456 `/scratch/stefan/7921153/working/3D/456' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)C(=O)N1C[C@@H]2CCN(C(=O)C3=CC(=O)[N-]O3)[C@@H]2C1) `REAL250005042347.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042347.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042347/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042347 none CC(O)C(=O)N1C[C@@H]2CCN(C(=O)C3=CC(=O)[N-]O3)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [24, 18, 24, 12, 18, 12, 12, 12, 12, 12, 12, 7, 1, 7, 1, 1, 1, 1, 1, 1, 11, 12, 12, 24, 24, 24, 24, 72, 12, 12, 12, 12, 12, 12, 1, 12, 12] 72 rigid atoms, others: [34, 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, 35, 36]) total number of confs: 153 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042347 none CC(O)C(=O)N1C[C@@H]2CCN(C(=O)C3=CC(=O)[N-]O3)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [10, 6, 10, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 12, 12, 12, 12, 12, 1, 1, 1, 10, 10, 10, 10, 30, 1, 1, 1, 1, 1, 1, 12, 1, 1] 72 rigid atoms, others: [32, 33, 3, 36, 5, 6, 7, 8, 9, 10, 11, 12, 35, 20, 21, 22, 28, 29, 30, 31] set([0, 1, 2, 34, 4, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27]) total number of confs: 83 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042347 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042347 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042347/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042347 Building REAL250005042348 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042348' /scratch/stefan/7921153/working/building/REAL250005042348 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042348 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042348/0 /scratch/stefan/7921153/working/building/REAL250005042348 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 457) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/457 `/scratch/stefan/7921153/working/3D/457' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)C(=O)N1C[C@@H]2CCN(C(=O)C3=CC(=O)[N-]O3)[C@@H]2C1) `REAL250005042348.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042348/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042348 none CC(=O)C(=O)N1C[C@@H]2CCN(C(=O)C3=CC(=O)[N-]O3)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [37, 27, 37, 19, 27, 19, 19, 19, 19, 19, 19, 9, 1, 9, 1, 1, 1, 1, 1, 1, 18, 19, 19, 37, 37, 37, 19, 19, 19, 19, 19, 19, 1, 19, 19] 37 rigid atoms, others: [32, 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, 33, 34]) total number of confs: 105 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042348 none CC(=O)C(=O)N1C[C@@H]2CCN(C(=O)C3=CC(=O)[N-]O3)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [16, 5, 16, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 19, 19, 19, 19, 19, 1, 1, 1, 17, 17, 17, 1, 1, 1, 1, 1, 1, 19, 1, 1] 37 rigid atoms, others: [33, 34, 3, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 4, 32, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25]) total number of confs: 79 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042348 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042348 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042348/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042348 Building REAL250005042349 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042349' /scratch/stefan/7921153/working/building/REAL250005042349 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042349 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042349/0 /scratch/stefan/7921153/working/building/REAL250005042349 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 458) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/458 `/scratch/stefan/7921153/working/3D/458' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=CC(=O)N1C[C@@H]2CCN(C(=O)C3=CC(=O)[N-]O3)[C@@H]2C1) `REAL250005042349.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042349/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042349 none CC=CC(=O)N1C[C@@H]2CCN(C(=O)C3=CC(=O)[N-]O3)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 26, 17, 26, 17, 17, 17, 17, 17, 17, 8, 1, 8, 1, 1, 1, 1, 1, 1, 16, 17, 17, 31, 31, 31, 31, 31, 17, 17, 17, 17, 17, 17, 1, 17, 17] 31 rigid atoms, others: [34, 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, 35, 36]) total number of confs: 81 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042349 none CC=CC(=O)N1C[C@@H]2CCN(C(=O)C3=CC(=O)[N-]O3)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [15, 14, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 17, 17, 17, 17, 17, 1, 1, 1, 15, 15, 15, 14, 14, 1, 1, 1, 1, 1, 1, 17, 1, 1] 31 rigid atoms, others: [32, 33, 3, 36, 5, 6, 7, 8, 9, 10, 11, 12, 35, 20, 21, 22, 28, 29, 30, 31] set([0, 1, 2, 34, 4, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042349 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042349 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042349/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042349 Building REAL250005042350 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042350' /scratch/stefan/7921153/working/building/REAL250005042350 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042350 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042350/0 /scratch/stefan/7921153/working/building/REAL250005042350 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 459) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/459 `/scratch/stefan/7921153/working/3D/459' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](O)C(=O)N1C[C@@H]2CCN(C(=O)C3=CC(=O)[N-]O3)[C@@H]2C1) `REAL250005042350.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042350.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042350/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042350 none C[C@H](O)C(=O)N1C[C@@H]2CCN(C(=O)C3=CC(=O)[N-]O3)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [25, 19, 25, 25, 13, 19, 13, 13, 13, 13, 13, 13, 8, 1, 8, 1, 1, 1, 1, 1, 1, 13, 13, 13, 25, 25, 25, 75, 13, 13, 13, 13, 13, 13, 1, 13, 13] 75 rigid atoms, others: [34, 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, 35, 36]) total number of confs: 155 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042350 none C[C@H](O)C(=O)N1C[C@@H]2CCN(C(=O)C3=CC(=O)[N-]O3)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [10, 6, 10, 10, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 13, 13, 13, 13, 13, 1, 1, 1, 10, 10, 10, 30, 1, 1, 1, 1, 1, 1, 13, 1, 1] 75 rigid atoms, others: [32, 33, 35, 4, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 36, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 34, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27]) total number of confs: 84 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042350 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042350 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042350/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042350 Building REAL250005042351 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042351' /scratch/stefan/7921153/working/building/REAL250005042351 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042351 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042351/0 /scratch/stefan/7921153/working/building/REAL250005042351 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 460) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/460 `/scratch/stefan/7921153/working/3D/460' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC(=O)N1C[C@@H]2CCN(C(=O)C3=CC(=O)[N-]O3)[C@@H]2C1) `REAL250005042351.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042351.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042351/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042351 none C=CCC(=O)N1C[C@@H]2CCN(C(=O)C3=CC(=O)[N-]O3)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 33, 19, 33, 19, 19, 19, 19, 19, 19, 9, 1, 9, 1, 1, 1, 1, 1, 1, 19, 19, 19, 60, 60, 60, 60, 60, 19, 19, 19, 19, 19, 19, 1, 19, 19] 60 rigid atoms, others: [34, 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, 35, 36]) total number of confs: 216 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042351 none C=CCC(=O)N1C[C@@H]2CCN(C(=O)C3=CC(=O)[N-]O3)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [32, 22, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 19, 19, 19, 19, 19, 1, 1, 1, 32, 32, 32, 22, 22, 1, 1, 1, 1, 1, 1, 19, 1, 1] 60 rigid atoms, others: [32, 33, 3, 36, 5, 6, 7, 8, 9, 10, 11, 12, 35, 20, 21, 22, 28, 29, 30, 31] set([0, 1, 2, 34, 4, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042351 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042351 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042351/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042351 Building REAL250005042352 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042352' /scratch/stefan/7921153/working/building/REAL250005042352 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042352 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042352/0 /scratch/stefan/7921153/working/building/REAL250005042352 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 461) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/461 `/scratch/stefan/7921153/working/3D/461' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CCC(=O)N1C[C@@H]2CCN(C(=O)C3=CC(=O)[N-]O3)[C@@H]2C1) `REAL250005042352.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042352/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042352 none N#CCC(=O)N1C[C@@H]2CCN(C(=O)C3=CC(=O)[N-]O3)[C@@H]2C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 30, 21, 30, 21, 21, 21, 21, 21, 21, 9, 1, 9, 1, 1, 1, 1, 1, 1, 21, 21, 21, 49, 49, 21, 21, 21, 21, 21, 21, 1, 21, 21] 49 rigid atoms, others: [12, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33]) total number of confs: 167 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042352 none N#CCC(=O)N1C[C@@H]2CCN(C(=O)C3=CC(=O)[N-]O3)[C@@H]2C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 21, 21, 21, 21, 21, 1, 1, 1, 19, 19, 1, 1, 1, 1, 1, 1, 21, 1, 1] 49 rigid atoms, others: [32, 33, 3, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 25, 26, 27, 28, 29, 30] set([0, 1, 2, 4, 13, 14, 15, 16, 17, 18, 19, 23, 24, 31]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042352 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042352 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042352/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042352 Building REAL250005042353 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042353' /scratch/stefan/7921153/working/building/REAL250005042353 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042353 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042353/0 /scratch/stefan/7921153/working/building/REAL250005042353 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 462) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/462 `/scratch/stefan/7921153/working/3D/462' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCF)N1C[C@@H]2CCN(C(=O)C3=CC(=O)[N-]O3)[C@@H]2C1) `REAL250005042353.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042353.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042353/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042353 none O=C(CCF)N1C[C@@H]2CCN(C(=O)C3=CC(=O)[N-]O3)[C@@H]2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'F', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 15, 8, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [33, 21, 33, 67, 67, 21, 21, 21, 21, 21, 21, 9, 1, 9, 1, 1, 1, 1, 1, 1, 20, 21, 21, 67, 67, 67, 67, 21, 21, 21, 21, 21, 21, 1, 21, 21] 67 rigid atoms, others: [33, 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, 34, 35]) total number of confs: 241 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042353 none O=C(CCF)N1C[C@@H]2CCN(C(=O)C3=CC(=O)[N-]O3)[C@@H]2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'F', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 15, 8, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 15, 23, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 21, 21, 21, 21, 21, 1, 1, 1, 15, 15, 23, 23, 1, 1, 1, 1, 1, 1, 21, 1, 1] 67 rigid atoms, others: [32, 1, 34, 35, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 27, 28, 29, 30, 31] set([0, 33, 2, 3, 4, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042353 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042353 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042353/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042353 Building REAL250005042354 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042354' /scratch/stefan/7921153/working/building/REAL250005042354 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042354 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042354/0 /scratch/stefan/7921153/working/building/REAL250005042354 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 463) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/463 `/scratch/stefan/7921153/working/3D/463' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](O)C(=O)N1C[C@@H]2CCN(C(=O)C3=CC(=O)[N-]O3)[C@@H]2C1) `REAL250005042354.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042354.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042354/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042354 none C[C@@H](O)C(=O)N1C[C@@H]2CCN(C(=O)C3=CC(=O)[N-]O3)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [37, 28, 37, 37, 13, 28, 13, 13, 13, 13, 13, 13, 7, 1, 7, 1, 1, 1, 1, 1, 1, 13, 13, 13, 37, 37, 37, 111, 13, 13, 13, 13, 13, 13, 1, 13, 13] 111 rigid atoms, others: [34, 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, 35, 36]) total number of confs: 230 number of broken/clashed sets: 15 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042354 none C[C@@H](O)C(=O)N1C[C@@H]2CCN(C(=O)C3=CC(=O)[N-]O3)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [15, 5, 15, 15, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 13, 13, 13, 13, 13, 1, 1, 1, 15, 15, 15, 45, 1, 1, 1, 1, 1, 1, 13, 1, 1] 111 rigid atoms, others: [32, 33, 35, 4, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 36, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 34, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27]) total number of confs: 121 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042354 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042354 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042354/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042354 Building REAL250005042355 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042355' /scratch/stefan/7921153/working/building/REAL250005042355 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042355 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042355/0 /scratch/stefan/7921153/working/building/REAL250005042355 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 464) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/464 `/scratch/stefan/7921153/working/3D/464' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(=O)N1C[C@@H]2CCN(C(=O)C3=CC(=O)[N-]O3)[C@@H]2C1) `REAL250005042355.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042355.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042355/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042355 none C=CC(=O)N1C[C@@H]2CCN(C(=O)C3=CC(=O)[N-]O3)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 14, 23, 14, 14, 14, 14, 14, 14, 8, 1, 8, 1, 1, 1, 1, 1, 1, 13, 14, 14, 23, 23, 23, 14, 14, 14, 14, 14, 14, 1, 14, 14] 23 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 31] 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, 32, 33]) total number of confs: 56 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042355 none C=CC(=O)N1C[C@@H]2CCN(C(=O)C3=CC(=O)[N-]O3)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 14, 14, 14, 14, 14, 1, 1, 1, 11, 10, 10, 1, 1, 1, 1, 1, 1, 14, 1, 1] 23 rigid atoms, others: [32, 33, 2, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 25, 26, 27, 28, 29, 30] set([0, 1, 3, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 31]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042355 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042355 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042355/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042355 Building REAL250005042356 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042356' /scratch/stefan/7921153/working/building/REAL250005042356 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042356 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042356/0 /scratch/stefan/7921153/working/building/REAL250005042356 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 465) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/465 `/scratch/stefan/7921153/working/3D/465' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O) `REAL250005042356.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042356.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042356/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042356 none CCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 237 conformations in input total number of sets (complete confs): 237 using faster count positions algorithm for large data unique positions, atoms: [79, 57, 57, 57, 30, 30, 30, 29, 9, 1, 9, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 79, 79, 79, 79, 79, 57, 29, 29, 1, 30, 30, 90] 237 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32]) total number of confs: 361 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042356 none CCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 237 conformations in input total number of sets (complete confs): 237 using faster count positions algorithm for large data unique positions, atoms: [34, 6, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 29, 29, 29, 29, 29, 1, 1, 1, 1, 34, 34, 34, 34, 34, 6, 1, 1, 29, 1, 1, 3] 237 rigid atoms, others: [4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 27, 28, 30, 31] set([0, 1, 2, 3, 32, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 29]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042356 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042356 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042356/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042356 Building REAL250005042357 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042357' /scratch/stefan/7921153/working/building/REAL250005042357 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042357 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042357/0 /scratch/stefan/7921153/working/building/REAL250005042357 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 466) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/466 `/scratch/stefan/7921153/working/3D/466' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O) `REAL250005042357.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042357/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042357 none COCCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 471 conformations in input total number of sets (complete confs): 471 using faster count positions algorithm for large data unique positions, atoms: [157, 157, 144, 64, 64, 64, 30, 30, 30, 29, 10, 1, 10, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 157, 157, 157, 157, 157, 144, 144, 64, 30, 30, 1, 30, 30, 90] 471 rigid atoms, others: [33, 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, 34, 35, 36]) total number of confs: 669 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042357 none COCCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 471 conformations in input total number of sets (complete confs): 471 using faster count positions algorithm for large data unique positions, atoms: [90, 67, 40, 6, 6, 6, 1, 1, 1, 1, 1, 1, 7, 7, 30, 30, 30, 30, 30, 1, 1, 1, 1, 90, 90, 90, 68, 68, 40, 40, 6, 1, 1, 30, 1, 1, 6] 471 rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 33, 36]) total number of confs: 385 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042357 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042357 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042357/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042357 Building REAL250005042358 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042358' /scratch/stefan/7921153/working/building/REAL250005042358 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042358 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042358/0 /scratch/stefan/7921153/working/building/REAL250005042358 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 467) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/467 `/scratch/stefan/7921153/working/3D/467' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O) `REAL250005042358.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042358.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042358/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042358 none CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 17, 13, 13, 13, 12, 6, 1, 6, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 17, 17, 17, 17, 12, 12, 1, 13, 13, 39] 51 rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29]) total number of confs: 78 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042358 none CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 1, 1, 5, 5, 12, 12, 12, 12, 12, 1, 1, 1, 1, 6, 6, 6, 6, 1, 1, 13, 1, 1, 3] 51 rigid atoms, others: [3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 24, 25, 27, 28] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 26, 29]) total number of confs: 38 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042358 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042358 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042358/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042358 Building REAL250005042359 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042359' /scratch/stefan/7921153/working/building/REAL250005042359 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042359 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042359/0 /scratch/stefan/7921153/working/building/REAL250005042359 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 468) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/468 `/scratch/stefan/7921153/working/3D/468' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O)C1CC1) `REAL250005042359.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042359/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042359 none O=C(N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O)C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 5, 5, 5, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 309 conformations in input total number of sets (complete confs): 309 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 32, 32, 32, 32, 77, 77, 103, 103, 103, 103, 103, 32, 32, 32, 32, 1, 1, 1, 12, 32, 32, 103, 32, 32, 96, 1, 1, 1, 1, 1] 309 rigid atoms, others: [32, 1, 33, 19, 20, 21, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 355 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: REAL250005042359 none O=C(N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O)C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 5, 5, 5, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 303 conformations in input total number of sets (complete confs): 303 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 29, 29, 29, 29, 9, 1, 9, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 50, 101, 101, 50, 29, 29, 1, 29, 29, 87, 101, 101, 101, 101, 101] 303 rigid atoms, others: [7, 9, 10, 11, 12, 13, 14, 25] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 363 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042359 none O=C(N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O)C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 5, 5, 5, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 303 conformations in input total number of sets (complete confs): 303 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 1, 1, 1, 1, 1, 1, 7, 7, 29, 29, 29, 29, 29, 1, 1, 1, 1, 7, 33, 33, 7, 1, 1, 29, 1, 1, 6, 33, 33, 33, 33, 33] 303 rigid atoms, others: [2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 23, 24, 26, 27] set([0, 1, 33, 32, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 25, 28, 29, 30, 31]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042359 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042359 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042359/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042359 Building REAL250005042360 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042360' /scratch/stefan/7921153/working/building/REAL250005042360 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042360 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042360/0 /scratch/stefan/7921153/working/building/REAL250005042360 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 469) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/469 `/scratch/stefan/7921153/working/3D/469' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O)C1CCC1) `REAL250005042360.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042360/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042360 none O=C(N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O)C1CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 219 conformations in input total number of sets (complete confs): 219 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 36, 36, 36, 36, 65, 65, 73, 73, 73, 73, 73, 36, 36, 36, 36, 1, 1, 1, 1, 12, 36, 36, 73, 36, 36, 108, 1, 1, 1, 1, 1, 1, 1] 219 rigid atoms, others: [32, 1, 34, 35, 36, 33, 19, 20, 21, 22, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 315 number of broken/clashed sets: 3 ./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: REAL250005042360 none O=C(N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O)C1CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 219 conformations in input total number of sets (complete confs): 219 using faster count positions algorithm for large data unique positions, atoms: [34, 34, 18, 18, 18, 17, 7, 1, 7, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 34, 73, 73, 73, 34, 17, 17, 1, 18, 18, 54, 73, 73, 73, 73, 73, 73, 73] 219 rigid atoms, others: [7, 9, 10, 11, 12, 13, 14, 26] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 257 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042360 none O=C(N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O)C1CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 219 conformations in input total number of sets (complete confs): 219 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 1, 1, 1, 1, 1, 1, 5, 5, 17, 17, 17, 18, 18, 1, 1, 1, 1, 7, 36, 36, 36, 7, 1, 1, 18, 1, 1, 3, 36, 36, 36, 36, 36, 36, 36] 219 rigid atoms, others: [2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 24, 25, 27, 28] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 26, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 119 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042360 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042360 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042360/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042360 Building REAL250005042361 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042361' /scratch/stefan/7921153/working/building/REAL250005042361 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042361 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042361/0 /scratch/stefan/7921153/working/building/REAL250005042361 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 470) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/470 `/scratch/stefan/7921153/working/3D/470' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1CC1)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O) `REAL250005042361.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042361.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042361/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042361 none O=C(CC1CC1)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 348 conformations in input total number of sets (complete confs): 348 using faster count positions algorithm for large data unique positions, atoms: [52, 52, 52, 102, 116, 116, 20, 21, 21, 20, 6, 1, 6, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 102, 102, 116, 116, 116, 116, 116, 52, 20, 20, 1, 21, 21, 63] 348 rigid atoms, others: [33, 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, 34, 35, 36]) total number of confs: 476 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: REAL250005042361 none O=C(CC1CC1)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 348 conformations in input total number of sets (complete confs): 348 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 52, 75, 75, 1, 1, 1, 1, 1, 1, 5, 5, 20, 21, 21, 21, 21, 1, 1, 1, 1, 52, 52, 75, 75, 75, 75, 75, 7, 1, 1, 20, 1, 1, 3] 348 rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 33, 36]) total number of confs: 295 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042361 none O=C(CC1CC1)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 348 conformations in input total number of sets (complete confs): 348 using faster count positions algorithm for large data unique positions, atoms: [22, 3, 1, 1, 1, 1, 22, 22, 75, 75, 75, 75, 113, 113, 116, 116, 116, 116, 116, 75, 75, 75, 75, 3, 3, 1, 1, 1, 1, 1, 22, 75, 75, 116, 75, 75, 225] 348 rigid atoms, others: [2, 3, 4, 5, 25, 26, 27, 28, 29] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 565 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042361 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042361 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042361/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042361 Building REAL250005042362 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042362' /scratch/stefan/7921153/working/building/REAL250005042362 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042362 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042362/0 /scratch/stefan/7921153/working/building/REAL250005042362 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 471) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/471 `/scratch/stefan/7921153/working/3D/471' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O) `REAL250005042362.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042362.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042362/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042362 none COCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 183 conformations in input total number of sets (complete confs): 183 using faster count positions algorithm for large data unique positions, atoms: [61, 61, 40, 40, 40, 16, 16, 16, 15, 8, 1, 8, 1, 1, 1, 1, 1, 1, 15, 16, 16, 16, 61, 61, 61, 61, 61, 40, 15, 16, 1, 15, 15, 48] 183 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33]) total number of confs: 256 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042362 none COCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 183 conformations in input total number of sets (complete confs): 183 using faster count positions algorithm for large data unique positions, atoms: [40, 28, 6, 6, 6, 1, 1, 1, 1, 1, 1, 5, 5, 15, 15, 16, 15, 15, 1, 1, 1, 1, 40, 40, 40, 28, 28, 6, 1, 1, 16, 1, 1, 6] 183 rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 28, 29, 31] set([0, 1, 2, 3, 4, 33, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 30]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042362 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042362 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042362/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042362 Building REAL250005042363 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042363' /scratch/stefan/7921153/working/building/REAL250005042363 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042363 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042363/0 /scratch/stefan/7921153/working/building/REAL250005042363 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 472) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/472 `/scratch/stefan/7921153/working/3D/472' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O) `REAL250005042363.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042363.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042363/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042363 none CCCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 363 conformations in input total number of sets (complete confs): 363 using faster count positions algorithm for large data unique positions, atoms: [121, 120, 64, 64, 64, 23, 23, 23, 23, 8, 1, 8, 1, 1, 1, 1, 1, 1, 23, 24, 24, 24, 121, 121, 121, 121, 121, 120, 120, 64, 23, 23, 1, 24, 24, 72] 363 rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35]) total number of confs: 495 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042363 none CCCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 363 conformations in input total number of sets (complete confs): 363 using faster count positions algorithm for large data unique positions, atoms: [61, 45, 7, 7, 7, 1, 1, 1, 1, 1, 1, 5, 5, 23, 23, 23, 23, 23, 1, 1, 1, 1, 69, 69, 69, 69, 69, 45, 45, 7, 1, 1, 23, 1, 1, 6] 363 rigid atoms, others: [33, 34, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 32, 35]) total number of confs: 364 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042363 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042363 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042363/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042363 Building REAL250005042364 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042364' /scratch/stefan/7921153/working/building/REAL250005042364 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042364 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042364/0 /scratch/stefan/7921153/working/building/REAL250005042364 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 473) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/473 `/scratch/stefan/7921153/working/3D/473' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O) `REAL250005042364.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042364.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042364/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042364 none CC(C)CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 369 conformations in input total number of sets (complete confs): 369 using faster count positions algorithm for large data unique positions, atoms: [122, 122, 123, 58, 58, 58, 26, 26, 26, 25, 8, 1, 8, 1, 1, 1, 1, 1, 1, 25, 26, 26, 26, 123, 123, 123, 123, 123, 123, 123, 122, 122, 58, 26, 25, 1, 25, 25, 78] 369 rigid atoms, others: [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, 34, 36, 37, 38]) total number of confs: 526 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042364 none CC(C)CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 369 conformations in input total number of sets (complete confs): 369 using faster count positions algorithm for large data unique positions, atoms: [34, 31, 42, 7, 7, 7, 1, 1, 1, 1, 1, 1, 6, 6, 25, 26, 26, 25, 25, 1, 1, 1, 1, 42, 42, 42, 42, 42, 42, 42, 31, 31, 7, 1, 1, 26, 1, 1, 6] 369 rigid atoms, others: [33, 34, 36, 37, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 38]) total number of confs: 264 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042364 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042364 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042364/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042364 Building REAL250005042365 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042365' /scratch/stefan/7921153/working/building/REAL250005042365 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042365 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042365/0 /scratch/stefan/7921153/working/building/REAL250005042365 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 474) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/474 `/scratch/stefan/7921153/working/3D/474' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O) `REAL250005042365.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042365/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042365 none CC1CC1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [60, 60, 60, 42, 42, 42, 16, 16, 16, 15, 6, 1, 6, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 60, 60, 60, 60, 60, 60, 60, 42, 15, 15, 1, 16, 16, 48] 180 rigid atoms, others: [33, 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, 34, 35, 36]) total number of confs: 214 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042365 none CC1CC1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [31, 31, 31, 6, 6, 6, 1, 1, 1, 1, 1, 1, 5, 5, 15, 15, 15, 16, 16, 1, 1, 1, 1, 31, 31, 31, 31, 31, 31, 31, 6, 1, 1, 15, 1, 1, 3] 180 rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 33, 36]) total number of confs: 103 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042365 none CC1CC1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 180 conformations in input total number of sets (complete confs): 180 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 10, 10, 10, 31, 31, 31, 31, 57, 57, 60, 60, 60, 60, 60, 31, 31, 31, 31, 2, 2, 2, 1, 1, 1, 1, 10, 31, 31, 60, 31, 31, 93] 180 rigid atoms, others: [0, 1, 2, 3, 4, 26, 27, 28, 29] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 262 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042365 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042365 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042365/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042365 Building REAL250005042366 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042366' /scratch/stefan/7921153/working/building/REAL250005042366 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042366 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042366/0 /scratch/stefan/7921153/working/building/REAL250005042366 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 475) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/475 `/scratch/stefan/7921153/working/3D/475' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O) `REAL250005042366.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042366/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042366 none CCOCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [134, 134, 129, 59, 59, 59, 26, 26, 26, 26, 9, 1, 9, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 134, 134, 134, 134, 134, 129, 129, 59, 26, 26, 1, 26, 26, 78] 402 rigid atoms, others: [33, 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, 34, 35, 36]) total number of confs: 539 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042366 none CCOCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [81, 75, 41, 6, 6, 6, 1, 1, 1, 1, 1, 1, 7, 7, 26, 26, 26, 26, 26, 1, 1, 1, 1, 81, 81, 81, 81, 81, 41, 41, 6, 1, 1, 26, 1, 1, 6] 402 rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 33, 36]) total number of confs: 270 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042366 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042366 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042366/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042366 Building REAL250005042367 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042367' /scratch/stefan/7921153/working/building/REAL250005042367 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042367 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042367/0 /scratch/stefan/7921153/working/building/REAL250005042367 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 476) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/476 `/scratch/stefan/7921153/working/3D/476' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)=CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O) `REAL250005042367.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042367/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042367 none CC(C)=CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 5, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 237 conformations in input total number of sets (complete confs): 237 using faster count positions algorithm for large data unique positions, atoms: [79, 79, 79, 53, 53, 53, 23, 23, 23, 22, 8, 1, 8, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 79, 79, 79, 79, 79, 79, 79, 53, 22, 22, 1, 22, 23, 69] 237 rigid atoms, others: [33, 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, 34, 35, 36]) total number of confs: 301 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042367 none CC(C)=CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 5, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 237 conformations in input total number of sets (complete confs): 237 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 25, 7, 7, 7, 1, 1, 1, 1, 1, 1, 6, 6, 22, 22, 22, 22, 22, 1, 1, 1, 1, 25, 25, 25, 25, 25, 25, 25, 7, 1, 1, 22, 1, 1, 3] 237 rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 33, 36]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042367 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042367 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042367/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042367 Building REAL250005042368 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042368' /scratch/stefan/7921153/working/building/REAL250005042368 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042368 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042368/0 /scratch/stefan/7921153/working/building/REAL250005042368 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 477) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/477 `/scratch/stefan/7921153/working/3D/477' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O) `REAL250005042368.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042368.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042368/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042368 none CCCCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [199, 200, 188, 73, 73, 73, 30, 30, 30, 30, 9, 1, 9, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 199, 201, 201, 201, 201, 200, 200, 188, 188, 73, 30, 30, 1, 30, 30, 90] 603 rigid atoms, others: [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, 34, 36, 37, 38]) total number of confs: 845 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042368 none CCCCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [100, 63, 43, 6, 6, 6, 1, 1, 1, 1, 1, 1, 7, 7, 30, 30, 30, 30, 30, 1, 1, 1, 1, 100, 104, 104, 99, 101, 74, 74, 43, 43, 6, 1, 1, 30, 1, 1, 6] 603 rigid atoms, others: [33, 34, 36, 37, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 38]) total number of confs: 573 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042368 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042368 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042368/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042368 Building REAL250005042369 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042369' /scratch/stefan/7921153/working/building/REAL250005042369 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042369 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042369/0 /scratch/stefan/7921153/working/building/REAL250005042369 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 478) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/478 `/scratch/stefan/7921153/working/3D/478' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O) `REAL250005042369.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042369.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042369/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042369 none CC(C)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 165 conformations in input total number of sets (complete confs): 165 using faster count positions algorithm for large data unique positions, atoms: [55, 42, 55, 42, 42, 18, 18, 19, 18, 7, 1, 7, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 55, 55, 55, 55, 55, 55, 55, 42, 18, 18, 1, 19, 19, 57] 165 rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35]) total number of confs: 244 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042369 none CC(C)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 165 conformations in input total number of sets (complete confs): 165 using faster count positions algorithm for large data unique positions, atoms: [23, 7, 23, 7, 7, 1, 1, 1, 1, 1, 1, 5, 5, 18, 18, 18, 19, 19, 1, 1, 1, 1, 23, 23, 23, 23, 23, 23, 23, 7, 1, 1, 18, 1, 1, 6] 165 rigid atoms, others: [33, 34, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 32, 35]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042369 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042369 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042369/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042369 Building REAL250005042370 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042370' /scratch/stefan/7921153/working/building/REAL250005042370 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042370 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042370/0 /scratch/stefan/7921153/working/building/REAL250005042370 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 479) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/479 `/scratch/stefan/7921153/working/3D/479' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O) `REAL250005042370.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042370.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042370/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042370 none CCC(C)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 309 conformations in input total number of sets (complete confs): 309 using faster count positions algorithm for large data unique positions, atoms: [103, 99, 52, 99, 52, 52, 21, 21, 21, 20, 6, 1, 6, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 103, 103, 103, 103, 103, 99, 99, 99, 99, 52, 20, 20, 1, 21, 21, 63] 309 rigid atoms, others: [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, 34, 36, 37, 38]) total number of confs: 427 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042370 none CCC(C)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 309 conformations in input total number of sets (complete confs): 309 using faster count positions algorithm for large data unique positions, atoms: [49, 39, 7, 39, 7, 7, 1, 1, 1, 1, 1, 1, 5, 5, 20, 20, 20, 20, 20, 1, 1, 1, 1, 55, 55, 55, 55, 55, 39, 39, 39, 39, 7, 1, 1, 21, 1, 1, 3] 309 rigid atoms, others: [33, 34, 36, 37, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 38]) total number of confs: 293 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042370 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042370 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042370/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042370 Building REAL250005042371 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042371' /scratch/stefan/7921153/working/building/REAL250005042371 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042371 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042371/0 /scratch/stefan/7921153/working/building/REAL250005042371 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 480) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/480 `/scratch/stefan/7921153/working/3D/480' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O) `REAL250005042371.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042371.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042371/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042371 none COC(C)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [56, 56, 43, 56, 43, 43, 24, 24, 24, 24, 8, 1, 8, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 56, 56, 56, 56, 56, 56, 56, 43, 24, 24, 1, 24, 24, 72] 168 rigid atoms, others: [33, 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, 34, 35, 36]) total number of confs: 238 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042371 none COC(C)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [34, 28, 6, 29, 6, 6, 1, 1, 1, 1, 1, 1, 7, 7, 24, 24, 24, 24, 24, 1, 1, 1, 1, 34, 34, 34, 29, 29, 29, 29, 6, 1, 1, 24, 1, 1, 6] 168 rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 33, 36]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042371 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042371 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042371/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042371 Building REAL250005042372 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042372' /scratch/stefan/7921153/working/building/REAL250005042372 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042372 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042372/0 /scratch/stefan/7921153/working/building/REAL250005042372 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 481) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/481 `/scratch/stefan/7921153/working/3D/481' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O) `REAL250005042372.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042372/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042372 none C=CCCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 182, 69, 69, 69, 29, 29, 29, 28, 10, 1, 10, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 201, 201, 201, 201, 201, 182, 182, 69, 29, 29, 1, 29, 29, 87] 603 rigid atoms, others: [33, 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, 34, 35, 36]) total number of confs: 852 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042372 none C=CCCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [132, 82, 43, 6, 6, 6, 1, 1, 1, 1, 1, 1, 7, 7, 29, 29, 29, 29, 29, 1, 1, 1, 1, 132, 132, 132, 82, 82, 43, 43, 6, 1, 1, 29, 1, 1, 6] 603 rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 33, 36]) total number of confs: 555 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042372 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042372 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042372/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042372 Building REAL250005042373 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042373' /scratch/stefan/7921153/working/building/REAL250005042373 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042373 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042373/0 /scratch/stefan/7921153/working/building/REAL250005042373 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 482) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/482 `/scratch/stefan/7921153/working/3D/482' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=C(C)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O) `REAL250005042373.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042373.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042373/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042373 none CC=C(C)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [66, 66, 39, 66, 39, 39, 14, 14, 15, 14, 5, 1, 5, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 66, 66, 66, 66, 66, 66, 66, 39, 14, 14, 1, 15, 15, 45] 198 rigid atoms, others: [33, 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, 34, 35, 36]) total number of confs: 231 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042373 none CC=C(C)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [37, 37, 7, 37, 7, 7, 1, 1, 1, 1, 1, 1, 5, 5, 14, 15, 15, 15, 15, 1, 1, 1, 1, 37, 37, 37, 37, 37, 37, 37, 7, 1, 1, 14, 1, 1, 3] 198 rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 33, 36]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042373 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042373 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042373/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042373 Building REAL250005042374 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042374' /scratch/stefan/7921153/working/building/REAL250005042374 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042374 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042374/0 /scratch/stefan/7921153/working/building/REAL250005042374 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 483) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/483 `/scratch/stefan/7921153/working/3D/483' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C(=O)N[C@@H]2CN(C(=O)C3=CC(=O)[N-]O3)C[C@H]2O)CC1) `REAL250005042374.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042374/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042374 none CC1(C(=O)N[C@@H]2CN(C(=O)C3=CC(=O)[N-]O3)C[C@H]2O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 225 conformations in input total number of sets (complete confs): 225 using faster count positions algorithm for large data unique positions, atoms: [75, 45, 45, 45, 22, 22, 23, 22, 8, 1, 8, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 75, 75, 75, 75, 75, 45, 22, 22, 1, 23, 23, 69, 75, 75, 75, 75] 225 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 291 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: REAL250005042374 none CC1(C(=O)N[C@@H]2CN(C(=O)C3=CC(=O)[N-]O3)C[C@H]2O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 225 conformations in input total number of sets (complete confs): 225 using faster count positions algorithm for large data unique positions, atoms: [28, 6, 6, 6, 1, 1, 1, 1, 1, 1, 5, 5, 22, 22, 22, 23, 23, 1, 1, 1, 1, 28, 28, 28, 28, 28, 6, 1, 1, 22, 1, 1, 6, 28, 28, 28, 28] 225 rigid atoms, others: [4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 27, 28, 30, 31] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 29, 32, 33, 34, 35, 36]) total number of confs: 107 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042374 none CC1(C(=O)N[C@@H]2CN(C(=O)C3=CC(=O)[N-]O3)C[C@H]2O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 225 conformations in input total number of sets (complete confs): 225 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 7, 7, 7, 28, 28, 28, 28, 66, 66, 75, 75, 75, 75, 75, 28, 28, 28, 28, 1, 1, 2, 2, 2, 7, 28, 28, 75, 28, 28, 84, 1, 1, 1, 1] 225 rigid atoms, others: [0, 1, 2, 35, 36, 33, 34, 21, 22] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 302 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042374 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042374 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042374/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042374 Building REAL250005042375 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042375' /scratch/stefan/7921153/working/building/REAL250005042375 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042375 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042375/0 /scratch/stefan/7921153/working/building/REAL250005042375 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 484) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/484 `/scratch/stefan/7921153/working/3D/484' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H]1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O) `REAL250005042375.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042375.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042375/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042375 none C[C@@H]1C[C@H]1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 237 conformations in input total number of sets (complete confs): 237 using faster count positions algorithm for large data unique positions, atoms: [79, 79, 79, 79, 39, 79, 39, 39, 19, 19, 19, 18, 7, 1, 7, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 79, 79, 79, 79, 79, 39, 18, 18, 1, 19, 19, 57] 237 rigid atoms, others: [33, 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, 34, 35, 36]) total number of confs: 272 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: REAL250005042375 none C[C@@H]1C[C@H]1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 237 conformations in input total number of sets (complete confs): 237 using faster count positions algorithm for large data unique positions, atoms: [43, 43, 43, 43, 7, 43, 7, 7, 1, 1, 1, 1, 1, 1, 5, 5, 18, 18, 18, 18, 18, 1, 1, 1, 1, 43, 43, 43, 43, 43, 7, 1, 1, 19, 1, 1, 3] 237 rigid atoms, others: [32, 34, 35, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 33, 36]) total number of confs: 132 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042375 none C[C@@H]1C[C@H]1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 237 conformations in input total number of sets (complete confs): 237 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 43, 43, 43, 43, 76, 76, 79, 79, 79, 79, 79, 43, 43, 43, 43, 2, 2, 2, 1, 1, 12, 43, 43, 79, 43, 43, 129] 237 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 358 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042375 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042375 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042375/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042375 Building REAL250005042376 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042376' /scratch/stefan/7921153/working/building/REAL250005042376 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042376 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042376/0 /scratch/stefan/7921153/working/building/REAL250005042376 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 485) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/485 `/scratch/stefan/7921153/working/3D/485' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@@H]1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O) `REAL250005042376.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042376.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042376/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042376 none C[C@H]1C[C@@H]1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 234 conformations in input total number of sets (complete confs): 234 using faster count positions algorithm for large data unique positions, atoms: [78, 78, 78, 78, 38, 78, 38, 38, 19, 19, 19, 19, 7, 1, 7, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 78, 78, 78, 78, 78, 38, 19, 19, 1, 19, 19, 57] 234 rigid atoms, others: [33, 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, 34, 35, 36]) total number of confs: 269 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: REAL250005042376 none C[C@H]1C[C@@H]1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 234 conformations in input total number of sets (complete confs): 234 using faster count positions algorithm for large data unique positions, atoms: [37, 37, 37, 37, 7, 37, 7, 7, 1, 1, 1, 1, 1, 1, 5, 5, 19, 19, 19, 19, 19, 1, 1, 1, 1, 37, 37, 37, 37, 37, 7, 1, 1, 19, 1, 1, 3] 234 rigid atoms, others: [32, 34, 35, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 33, 36]) total number of confs: 119 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042376 none C[C@H]1C[C@@H]1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 234 conformations in input total number of sets (complete confs): 234 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 37, 37, 37, 37, 71, 71, 78, 78, 78, 78, 78, 37, 37, 37, 37, 2, 2, 2, 1, 1, 11, 37, 37, 78, 37, 37, 111] 234 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 332 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042376 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042376 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042376/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042376 Building REAL250005042377 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042377' /scratch/stefan/7921153/working/building/REAL250005042377 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042377 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042377/0 /scratch/stefan/7921153/working/building/REAL250005042377 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 486) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/486 `/scratch/stefan/7921153/working/3D/486' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O) `REAL250005042377.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042377.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042377/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042377 none NC(=O)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 6, 6, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [47, 41, 47, 41, 41, 24, 23, 24, 23, 7, 1, 7, 1, 1, 1, 1, 1, 1, 23, 24, 24, 24, 47, 47, 41, 23, 23, 1, 23, 23, 72] 141 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30]) total number of confs: 195 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042377 none NC(=O)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 6, 6, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [20, 6, 20, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 23, 23, 23, 23, 23, 1, 1, 1, 1, 20, 20, 6, 1, 1, 23, 1, 1, 3] 141 rigid atoms, others: [5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 25, 26, 28, 29] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 27, 30]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042377 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042377 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042377/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042377 Building REAL250005042378 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042378' /scratch/stefan/7921153/working/building/REAL250005042378 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042378 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042378/0 /scratch/stefan/7921153/working/building/REAL250005042378 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 487) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/487 `/scratch/stefan/7921153/working/3D/487' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O) `REAL250005042378.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042378.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042378/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042378 none CC(C)(C)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [26, 22, 26, 26, 22, 22, 14, 14, 14, 13, 6, 1, 6, 1, 1, 1, 1, 1, 1, 13, 14, 14, 14, 26, 26, 26, 26, 26, 26, 26, 26, 26, 22, 13, 14, 1, 13, 13, 42] 78 rigid atoms, others: [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, 34, 36, 37, 38]) total number of confs: 122 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042378 none CC(C)(C)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [12, 6, 12, 12, 6, 6, 1, 1, 1, 1, 1, 1, 5, 5, 13, 14, 14, 14, 13, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 1, 1, 14, 1, 1, 6] 78 rigid atoms, others: [33, 34, 36, 37, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 38]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042378 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042378 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042378/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042378 Building REAL250005042379 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042379' /scratch/stefan/7921153/working/building/REAL250005042379 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042379 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042379/0 /scratch/stefan/7921153/working/building/REAL250005042379 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 488) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/488 `/scratch/stefan/7921153/working/3D/488' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O) `REAL250005042379.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042379.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042379/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042379 none C=CCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [100, 100, 58, 58, 58, 26, 26, 26, 25, 9, 1, 9, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 100, 100, 100, 100, 100, 58, 25, 25, 1, 26, 26, 78] 300 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33]) total number of confs: 431 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042379 none C=CCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [60, 37, 6, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 25, 25, 25, 25, 25, 1, 1, 1, 1, 60, 60, 60, 37, 37, 6, 1, 1, 26, 1, 1, 3] 300 rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 28, 29, 31] set([0, 1, 2, 3, 4, 33, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 30]) total number of confs: 240 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042379 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042379 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042379/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042379 Building REAL250005042380 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042380' /scratch/stefan/7921153/working/building/REAL250005042380 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005042380 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042380/0 /scratch/stefan/7921153/working/building/REAL250005042380 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 489) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/489 `/scratch/stefan/7921153/working/3D/489' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[NH+](C)CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O) `REAL250005042380.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042380.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042380/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042380 none C[NH+](C)CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 1, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [18, 18, 18, 18, 16, 16, 16, 10, 10, 10, 9, 5, 1, 5, 1, 1, 1, 1, 1, 1, 9, 10, 10, 10, 18, 18, 18, 18, 18, 18, 18, 18, 16, 10, 9, 1, 9, 9, 30] 54 rigid atoms, others: [35, 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, 36, 37, 38]) total number of confs: 83 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042380 none C[NH+](C)CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 1, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [16, 15, 16, 16, 6, 6, 6, 1, 1, 1, 1, 1, 1, 4, 4, 9, 10, 10, 9, 9, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16, 15, 15, 6, 1, 1, 10, 1, 1, 6] 54 rigid atoms, others: [33, 34, 36, 37, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 38]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042380 /scratch/stefan/7921153/working /scratch/stefan/7921153 mkdir: created directory `1' /scratch/stefan/7921153/working/building/REAL250005042380/1 /scratch/stefan/7921153/working/building/REAL250005042380 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 1 (index: 490) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/490 `/scratch/stefan/7921153/working/3D/490' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O) `REAL250005042380.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005042380.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042380/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042380 none CN(C)CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 204 conformations in input total number of sets (complete confs): 204 using faster count positions algorithm for large data unique positions, atoms: [68, 66, 68, 34, 34, 34, 19, 19, 19, 19, 9, 1, 9, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 68, 68, 68, 68, 68, 68, 66, 66, 34, 19, 19, 1, 19, 19, 57] 204 rigid atoms, others: [34, 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, 35, 36, 37]) total number of confs: 302 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042380 none CN(C)CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 204 conformations in input total number of sets (complete confs): 204 using faster count positions algorithm for large data unique positions, atoms: [34, 28, 34, 6, 6, 6, 1, 1, 1, 1, 1, 1, 7, 7, 19, 19, 19, 19, 19, 1, 1, 1, 1, 34, 34, 34, 34, 34, 34, 28, 28, 6, 1, 1, 19, 1, 1, 6] 204 rigid atoms, others: [32, 33, 35, 36, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 37]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042380 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042380 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 1: /scratch/stefan/7921153/working/building/REAL250005042380/1.* 0: /scratch/stefan/7921153/working/building/REAL250005042380/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042380 Building REAL250005042381 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042381' /scratch/stefan/7921153/working/building/REAL250005042381 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042381 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042381/0 /scratch/stefan/7921153/working/building/REAL250005042381 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 491) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/491 `/scratch/stefan/7921153/working/3D/491' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(O)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O) `REAL250005042381.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042381/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:2-3 Rotatable hydrogens reported. Reducing confs by a factor of 3 WARNING:root:Setting energy window to 12 and max confs to 66 ('energy: ', 12.0) ('conf: ', 66) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042381 none C=CC(O)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [67, 67, 41, 67, 41, 41, 21, 21, 21, 20, 8, 1, 8, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 67, 67, 67, 67, 201, 41, 20, 20, 1, 21, 21, 63] 603 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 31] 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, 32, 33, 34]) total number of confs: 494 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042381 none C=CC(O)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [41, 26, 6, 26, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 20, 20, 20, 20, 20, 1, 1, 1, 1, 41, 41, 41, 26, 78, 6, 1, 1, 20, 1, 1, 3] 603 rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 29, 30] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 34, 23, 24, 25, 26, 27, 28, 31]) total number of confs: 247 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042381 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042381 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042381/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042381 Building REAL250005042382 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042382' /scratch/stefan/7921153/working/building/REAL250005042382 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042382 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042382/0 /scratch/stefan/7921153/working/building/REAL250005042382 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 492) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/492 `/scratch/stefan/7921153/working/3D/492' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O)C1COC1) `REAL250005042382.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042382/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042382 none O=C(N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O)C1COC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 5, 5, 12, 5, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [11, 1, 11, 11, 37, 37, 37, 37, 60, 60, 64, 64, 64, 64, 64, 37, 37, 37, 37, 1, 1, 1, 1, 11, 37, 37, 64, 37, 37, 111, 1, 1, 1, 1, 1] 192 rigid atoms, others: [32, 1, 34, 33, 19, 20, 21, 22, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 294 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: REAL250005042382 none O=C(N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O)C1COC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 5, 5, 12, 5, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [32, 32, 14, 14, 15, 14, 6, 1, 6, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 32, 64, 64, 64, 32, 14, 14, 1, 15, 15, 45, 64, 64, 64, 64, 64] 192 rigid atoms, others: [7, 9, 10, 11, 12, 13, 14, 26] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 229 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042382 none O=C(N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O)C1COC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 5, 5, 12, 5, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [7, 7, 1, 1, 1, 1, 1, 1, 5, 5, 14, 15, 15, 15, 15, 1, 1, 1, 1, 7, 37, 37, 37, 7, 1, 1, 14, 1, 1, 3, 37, 37, 37, 37, 37] 192 rigid atoms, others: [2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 24, 25, 27, 28] set([0, 1, 34, 33, 32, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 26, 29, 30, 31]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042382 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042382 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042382/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042382 Building REAL250005042383 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042383' /scratch/stefan/7921153/working/building/REAL250005042383 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042383 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042383/0 /scratch/stefan/7921153/working/building/REAL250005042383 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 493) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/493 `/scratch/stefan/7921153/working/3D/493' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H](C)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O) `REAL250005042383.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042383.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042383/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042383 none CO[C@H](C)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [56, 56, 42, 56, 56, 42, 42, 24, 24, 24, 23, 9, 1, 9, 1, 1, 1, 1, 1, 1, 23, 24, 24, 24, 56, 56, 56, 56, 56, 56, 42, 23, 23, 1, 23, 23, 72] 168 rigid atoms, others: [33, 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, 34, 35, 36]) total number of confs: 244 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042383 none CO[C@H](C)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [35, 28, 6, 30, 30, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 23, 23, 24, 23, 23, 1, 1, 1, 1, 35, 35, 35, 30, 30, 30, 6, 1, 1, 23, 1, 1, 3] 168 rigid atoms, others: [32, 34, 35, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 33, 36]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042383 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042383 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042383/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042383 Building REAL250005042384 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042384' /scratch/stefan/7921153/working/building/REAL250005042384 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042384 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042384/0 /scratch/stefan/7921153/working/building/REAL250005042384 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 494) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/494 `/scratch/stefan/7921153/working/3D/494' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC=CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O) `REAL250005042384.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042384/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042384 none CCC=CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 351 conformations in input total number of sets (complete confs): 351 using faster count positions algorithm for large data unique positions, atoms: [117, 96, 96, 61, 61, 61, 28, 28, 28, 28, 9, 1, 9, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 117, 117, 117, 117, 117, 96, 96, 61, 28, 28, 1, 28, 28, 84] 351 rigid atoms, others: [33, 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, 34, 35, 36]) total number of confs: 480 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042384 none CCC=CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 351 conformations in input total number of sets (complete confs): 351 using faster count positions algorithm for large data unique positions, atoms: [62, 35, 35, 6, 6, 6, 1, 1, 1, 1, 1, 1, 7, 7, 28, 28, 28, 28, 28, 1, 1, 1, 1, 62, 62, 62, 62, 62, 35, 35, 6, 1, 1, 28, 1, 1, 6] 351 rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 33, 36]) total number of confs: 269 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042384 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042384 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042384/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042384 Building REAL250005042385 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042385' /scratch/stefan/7921153/working/building/REAL250005042385 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types Protomer extracton resulted in 0 protomers Marking REAL250005042385 as failed and skipping /scratch/stefan/7921153/working /scratch/stefan/7921153 `/scratch/stefan/7921153/working/building/REAL250005042385' -> `/scratch/stefan/7921153/failed/REAL250005042385' Building REAL250005042386 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042386' /scratch/stefan/7921153/working/building/REAL250005042386 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042386 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042386/0 /scratch/stefan/7921153/working/building/REAL250005042386 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 495) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/495 `/scratch/stefan/7921153/working/3D/495' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CO)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O) `REAL250005042386.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042386/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:2-3 Rotatable hydrogens reported. Reducing confs by a factor of 3 WARNING:root:Setting energy window to 12 and max confs to 66 ('energy: ', 12.0) ('conf: ', 66) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042386 none O=C(CO)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 7, 4, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 414 conformations in input total number of sets (complete confs): 414 using faster count positions algorithm for large data unique positions, atoms: [45, 45, 45, 46, 26, 26, 26, 25, 8, 1, 8, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 46, 46, 138, 45, 25, 25, 1, 26, 26, 78] 414 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30]) total number of confs: 328 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042386 none O=C(CO)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 7, 4, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 414 conformations in input total number of sets (complete confs): 414 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 24, 1, 1, 1, 1, 1, 1, 6, 6, 25, 25, 25, 25, 25, 1, 1, 1, 1, 24, 24, 72, 7, 1, 1, 26, 1, 1, 3] 414 rigid atoms, others: [4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 25, 26, 28, 29] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 27, 30]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042386 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042386 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042386/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042386 Building REAL250005042387 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042387' /scratch/stefan/7921153/working/building/REAL250005042387 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042387 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042387/0 /scratch/stefan/7921153/working/building/REAL250005042387 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 496) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/496 `/scratch/stefan/7921153/working/3D/496' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O) `REAL250005042387.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042387/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:2-3 Rotatable hydrogens reported. Reducing confs by a factor of 3 WARNING:root:Setting energy window to 12 and max confs to 66 ('energy: ', 12.0) ('conf: ', 66) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042387 none CC(O)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 342 conformations in input total number of sets (complete confs): 342 using faster count positions algorithm for large data unique positions, atoms: [38, 28, 38, 28, 28, 17, 17, 17, 16, 6, 1, 6, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 38, 38, 38, 38, 114, 28, 16, 16, 1, 17, 17, 51] 342 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33]) total number of confs: 280 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042387 none CC(O)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 342 conformations in input total number of sets (complete confs): 342 using faster count positions algorithm for large data unique positions, atoms: [25, 6, 25, 6, 6, 1, 1, 1, 1, 1, 1, 5, 5, 16, 16, 16, 16, 16, 1, 1, 1, 1, 25, 25, 25, 25, 75, 6, 1, 1, 17, 1, 1, 3] 342 rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 28, 29, 31] set([0, 1, 2, 3, 4, 33, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 30]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042387 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042387 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042387/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042387 Building REAL250005042388 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042388' /scratch/stefan/7921153/working/building/REAL250005042388 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042388 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042388/0 /scratch/stefan/7921153/working/building/REAL250005042388 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 497) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/497 `/scratch/stefan/7921153/working/3D/497' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O)C1CC1F) `REAL250005042388.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042388/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042388 none O=C(N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O)C1CC1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 5, 5, 5, 15, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 342 conformations in input total number of sets (complete confs): 342 using faster count positions algorithm for large data unique positions, atoms: [13, 1, 13, 13, 50, 50, 50, 50, 100, 100, 114, 114, 114, 114, 114, 50, 50, 50, 50, 1, 1, 1, 1, 13, 50, 50, 114, 50, 50, 150, 1, 1, 1, 1] 342 rigid atoms, others: [32, 1, 33, 19, 20, 21, 22, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 462 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: REAL250005042388 none O=C(N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O)C1CC1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 5, 5, 5, 15, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 342 conformations in input total number of sets (complete confs): 342 using faster count positions algorithm for large data unique positions, atoms: [62, 62, 26, 25, 26, 25, 9, 1, 9, 1, 1, 1, 1, 1, 1, 25, 26, 26, 26, 62, 114, 114, 114, 62, 25, 25, 1, 25, 25, 78, 114, 114, 114, 114] 342 rigid atoms, others: [7, 9, 10, 11, 12, 13, 14, 26] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 396 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042388 none O=C(N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O)C1CC1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 5, 5, 5, 15, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 342 conformations in input total number of sets (complete confs): 342 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 1, 1, 1, 1, 1, 1, 6, 6, 25, 25, 25, 25, 25, 1, 1, 1, 1, 7, 50, 50, 50, 7, 1, 1, 25, 1, 1, 3, 50, 50, 50, 50] 342 rigid atoms, others: [2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 24, 25, 27, 28] set([0, 1, 33, 32, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 26, 29, 30, 31]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042388 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042388 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042388/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042388 Building REAL250005042389 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042389' /scratch/stefan/7921153/working/building/REAL250005042389 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042389 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042389/0 /scratch/stefan/7921153/working/building/REAL250005042389 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 498) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/498 `/scratch/stefan/7921153/working/3D/498' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCF)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O) `REAL250005042389.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042389/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042389 none O=C(CCF)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'F', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 15, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 534 conformations in input total number of sets (complete confs): 534 using faster count positions algorithm for large data unique positions, atoms: [91, 91, 91, 178, 178, 34, 34, 34, 33, 10, 1, 10, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 178, 178, 178, 178, 91, 34, 34, 1, 34, 34, 102] 534 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32]) total number of confs: 725 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042389 none O=C(CCF)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'F', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 15, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 534 conformations in input total number of sets (complete confs): 534 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 46, 85, 1, 1, 1, 1, 1, 1, 7, 7, 34, 34, 34, 34, 34, 1, 1, 1, 1, 46, 46, 85, 85, 7, 1, 1, 34, 1, 1, 6] 534 rigid atoms, others: [5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 27, 28, 30, 31] set([0, 1, 2, 3, 4, 32, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 29]) total number of confs: 410 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042389 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042389 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042389/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042389 Building REAL250005042390 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042390' /scratch/stefan/7921153/working/building/REAL250005042390 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042390 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042390/0 /scratch/stefan/7921153/working/building/REAL250005042390 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 499) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/499 `/scratch/stefan/7921153/working/3D/499' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(C=CCF)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O) `REAL250005042390.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042390.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042390/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042390 none O=C(C=CCF)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 1, 1, 5, 15, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 207 conformations in input total number of sets (complete confs): 207 using faster count positions algorithm for large data unique positions, atoms: [45, 45, 45, 68, 68, 69, 22, 22, 22, 22, 8, 1, 8, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 68, 68, 69, 69, 45, 22, 22, 1, 22, 22, 66] 207 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33]) total number of confs: 253 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042390 none O=C(C=CCF)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 1, 1, 5, 15, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 207 conformations in input total number of sets (complete confs): 207 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 24, 24, 46, 1, 1, 1, 1, 1, 1, 7, 7, 22, 22, 22, 22, 22, 1, 1, 1, 1, 24, 24, 46, 46, 6, 1, 1, 22, 1, 1, 6] 207 rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 28, 29, 31] set([0, 1, 2, 3, 4, 5, 33, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 30]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042390 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042390 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042390/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042390 Building REAL250005042391 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042391' /scratch/stefan/7921153/working/building/REAL250005042391 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042391 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042391/0 /scratch/stefan/7921153/working/building/REAL250005042391 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 500) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/500 `/scratch/stefan/7921153/working/3D/500' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O) `REAL250005042391.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042391/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042391 none C#CCCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 369 conformations in input total number of sets (complete confs): 369 using faster count positions algorithm for large data unique positions, atoms: [123, 123, 112, 55, 55, 55, 19, 19, 20, 19, 6, 1, 6, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 123, 123, 123, 112, 112, 55, 19, 19, 1, 20, 20, 60] 369 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 31] 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, 32, 33, 34]) total number of confs: 516 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042391 none C#CCCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 369 conformations in input total number of sets (complete confs): 369 using faster count positions algorithm for large data unique positions, atoms: [69, 69, 42, 7, 7, 7, 1, 1, 1, 1, 1, 1, 5, 5, 19, 19, 19, 20, 20, 1, 1, 1, 1, 69, 69, 69, 42, 42, 7, 1, 1, 19, 1, 1, 3] 369 rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 29, 30] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 34, 23, 24, 25, 26, 27, 28, 31]) total number of confs: 310 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042391 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042391 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042391/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042391 Building REAL250005042392 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042392' /scratch/stefan/7921153/working/building/REAL250005042392 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042392 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042392/0 /scratch/stefan/7921153/working/building/REAL250005042392 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 501) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/501 `/scratch/stefan/7921153/working/3D/501' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O)C1CCO1) `REAL250005042392.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042392.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042392/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042392 none O=C(N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O)C1CCO1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 5, 5, 5, 12, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [8, 1, 8, 8, 19, 19, 19, 19, 30, 30, 31, 31, 31, 31, 31, 19, 19, 19, 19, 1, 1, 1, 1, 8, 19, 19, 31, 19, 19, 57, 1, 1, 1, 1, 1] 93 rigid atoms, others: [32, 1, 34, 33, 19, 20, 21, 22, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 144 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: REAL250005042392 none O=C(N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O)C1CCO1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 5, 5, 5, 12, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [28, 28, 17, 17, 17, 16, 6, 1, 6, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 28, 31, 31, 31, 28, 16, 16, 1, 17, 17, 51, 31, 31, 31, 31, 31] 93 rigid atoms, others: [7, 9, 10, 11, 12, 13, 14, 26] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 127 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042392 none O=C(N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O)C1CCO1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 5, 5, 5, 12, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 1, 1, 1, 1, 1, 1, 5, 5, 16, 16, 16, 16, 16, 1, 1, 1, 1, 7, 19, 19, 19, 7, 1, 1, 16, 1, 1, 3, 19, 19, 19, 19, 19] 93 rigid atoms, others: [2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 24, 25, 27, 28] set([0, 1, 34, 33, 32, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 26, 29, 30, 31]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042392 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042392 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042392/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042392 Building REAL250005042393 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042393' /scratch/stefan/7921153/working/building/REAL250005042393 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042393 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042393/0 /scratch/stefan/7921153/working/building/REAL250005042393 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 502) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/502 `/scratch/stefan/7921153/working/3D/502' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(O)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O) `REAL250005042393.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042393.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042393/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:2-3 Rotatable hydrogens reported. Reducing confs by a factor of 3 WARNING:root:Setting energy window to 12 and max confs to 66 ('energy: ', 12.0) ('conf: ', 66) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042393 none CC(C)(O)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 423 conformations in input total number of sets (complete confs): 423 using faster count positions algorithm for large data unique positions, atoms: [47, 36, 47, 47, 36, 36, 20, 20, 20, 20, 7, 1, 7, 1, 1, 1, 1, 1, 1, 19, 20, 20, 20, 47, 47, 47, 47, 47, 47, 141, 36, 20, 20, 1, 19, 19, 60] 423 rigid atoms, others: [33, 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, 34, 35, 36]) total number of confs: 347 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042393 none CC(C)(O)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 423 conformations in input total number of sets (complete confs): 423 using faster count positions algorithm for large data unique positions, atoms: [29, 7, 29, 28, 7, 7, 1, 1, 1, 1, 1, 1, 5, 5, 20, 20, 20, 20, 19, 1, 1, 1, 1, 29, 29, 29, 29, 29, 29, 87, 7, 1, 1, 20, 1, 1, 3] 423 rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 33, 36]) total number of confs: 216 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042393 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042393 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042393/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042393 Building REAL250005042394 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042394' /scratch/stefan/7921153/working/building/REAL250005042394 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042394 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042394/0 /scratch/stefan/7921153/working/building/REAL250005042394 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 503) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/503 `/scratch/stefan/7921153/working/3D/503' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O) `REAL250005042394.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042394.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042394/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042394 none CC1=CC1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 435 conformations in input total number of sets (complete confs): 435 using faster count positions algorithm for large data unique positions, atoms: [145, 145, 145, 66, 66, 66, 28, 28, 28, 27, 8, 1, 8, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 145, 145, 145, 145, 145, 66, 27, 27, 1, 28, 28, 84] 435 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 31] 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, 32, 33, 34]) total number of confs: 484 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: REAL250005042394 none CC1=CC1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 435 conformations in input total number of sets (complete confs): 435 using faster count positions algorithm for large data unique positions, atoms: [62, 62, 62, 7, 7, 7, 1, 1, 1, 1, 1, 1, 6, 6, 27, 27, 27, 27, 27, 1, 1, 1, 1, 62, 62, 62, 62, 62, 7, 1, 1, 28, 1, 1, 6] 435 rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 29, 30] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 34, 23, 24, 25, 26, 27, 28, 31]) total number of confs: 184 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042394 none CC1=CC1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 435 conformations in input total number of sets (complete confs): 435 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 13, 13, 13, 62, 62, 62, 62, 121, 121, 145, 145, 145, 145, 145, 62, 62, 62, 62, 2, 2, 2, 1, 1, 13, 62, 62, 145, 62, 62, 186] 435 rigid atoms, others: [0, 1, 2, 3, 4, 26, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 577 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042394 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042394 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042394/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042394 Building REAL250005042395 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042395' /scratch/stefan/7921153/working/building/REAL250005042395 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042395 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042395/0 /scratch/stefan/7921153/working/building/REAL250005042395 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 504) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/504 `/scratch/stefan/7921153/working/3D/504' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](O)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O) `REAL250005042395.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042395.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042395/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:2-3 Rotatable hydrogens reported. Reducing confs by a factor of 3 WARNING:root:Setting energy window to 12 and max confs to 66 ('energy: ', 12.0) ('conf: ', 66) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042395 none C[C@@H](O)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 360 conformations in input total number of sets (complete confs): 360 using faster count positions algorithm for large data unique positions, atoms: [40, 30, 40, 40, 30, 30, 17, 17, 17, 16, 7, 1, 7, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 40, 40, 40, 120, 30, 16, 16, 1, 17, 17, 51] 360 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33]) total number of confs: 300 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042395 none C[C@@H](O)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 360 conformations in input total number of sets (complete confs): 360 using faster count positions algorithm for large data unique positions, atoms: [26, 7, 26, 26, 7, 7, 1, 1, 1, 1, 1, 1, 5, 5, 16, 16, 16, 16, 16, 1, 1, 1, 1, 26, 26, 26, 78, 7, 1, 1, 17, 1, 1, 3] 360 rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 28, 29, 31] set([0, 1, 2, 3, 4, 5, 33, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 30]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042395 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042395 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042395/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042395 Building REAL250005042396 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042396' /scratch/stefan/7921153/working/building/REAL250005042396 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042396 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042396/0 /scratch/stefan/7921153/working/building/REAL250005042396 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 505) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/505 `/scratch/stefan/7921153/working/3D/505' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(C=CCO)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O) `REAL250005042396.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042396.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042396/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:2-3 Rotatable hydrogens reported. Reducing confs by a factor of 3 WARNING:root:Setting energy window to 12 and max confs to 66 ('energy: ', 12.0) ('conf: ', 66) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042396 none O=C(C=CCO)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 1, 1, 5, 12, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 7, 7, 7, 4, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [38, 38, 38, 65, 65, 67, 13, 13, 13, 12, 5, 1, 5, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 65, 65, 67, 67, 201, 38, 12, 12, 1, 13, 13, 39] 603 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 31] 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, 32, 33, 34]) total number of confs: 433 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042396 none O=C(C=CCO)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 1, 1, 5, 12, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 7, 7, 7, 4, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 28, 28, 47, 1, 1, 1, 1, 1, 1, 5, 5, 12, 12, 12, 12, 12, 1, 1, 1, 1, 28, 28, 47, 47, 141, 7, 1, 1, 13, 1, 1, 3] 603 rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 29, 30] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 34, 23, 24, 25, 26, 27, 28, 31]) total number of confs: 329 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042396 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042396 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042396/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042396 Building REAL250005042397 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042397' /scratch/stefan/7921153/working/building/REAL250005042397 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042397 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042397/0 /scratch/stefan/7921153/working/building/REAL250005042397 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 506) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/506 `/scratch/stefan/7921153/working/3D/506' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O)C1=CCC1) `REAL250005042397.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042397.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042397/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042397 none O=C(N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O)C1=CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 1, 1, 5, 5, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [6, 1, 6, 6, 14, 14, 14, 14, 27, 27, 36, 36, 36, 36, 36, 14, 14, 14, 14, 1, 1, 1, 1, 6, 14, 14, 36, 14, 14, 42, 1, 1, 1, 1, 1] 108 rigid atoms, others: [32, 1, 34, 33, 19, 20, 21, 22, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 134 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: REAL250005042397 none O=C(N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O)C1=CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 1, 1, 5, 5, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [36, 36, 20, 20, 20, 20, 7, 1, 7, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 36, 36, 36, 36, 36, 20, 20, 1, 20, 20, 60, 36, 36, 36, 36, 36] 108 rigid atoms, others: [7, 9, 10, 11, 12, 13, 14, 26] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 150 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042397 none O=C(N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O)C1=CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 1, 1, 5, 5, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [7, 7, 1, 1, 1, 1, 1, 1, 7, 7, 20, 20, 20, 20, 20, 1, 1, 1, 1, 7, 14, 14, 14, 7, 1, 1, 20, 1, 1, 6, 14, 14, 14, 14, 14] 108 rigid atoms, others: [2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 24, 25, 27, 28] set([0, 1, 34, 33, 32, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 26, 29, 30, 31]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042397 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042397 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042397/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042397 Building REAL250005042398 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042398' /scratch/stefan/7921153/working/building/REAL250005042398 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042398 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042398/0 /scratch/stefan/7921153/working/building/REAL250005042398 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 507) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/507 `/scratch/stefan/7921153/working/3D/507' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CON=CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O) `REAL250005042398.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042398/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042398 none CON=CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 8, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [31, 31, 31, 25, 25, 25, 14, 14, 14, 13, 6, 1, 6, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 31, 31, 31, 31, 25, 13, 13, 1, 14, 14, 42] 93 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33]) total number of confs: 123 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042398 none CON=CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 8, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [20, 19, 19, 6, 6, 6, 1, 1, 1, 1, 1, 1, 4, 4, 13, 13, 13, 13, 13, 1, 1, 1, 1, 20, 20, 20, 19, 6, 1, 1, 14, 1, 1, 3] 93 rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 28, 29, 31] set([0, 1, 2, 3, 4, 5, 33, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 30]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042398 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042398 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042398/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042398 Building REAL250005042399 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042399' /scratch/stefan/7921153/working/building/REAL250005042399 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042399 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042399/0 /scratch/stefan/7921153/working/building/REAL250005042399 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 508) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/508 `/scratch/stefan/7921153/working/3D/508' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O)C1(F)CC1) `REAL250005042399.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042399.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042399/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042399 none O=C(N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O)C1(F)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 5, 15, 5, 5, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 327 conformations in input total number of sets (complete confs): 327 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 47, 47, 47, 47, 93, 93, 109, 109, 109, 109, 109, 47, 47, 47, 47, 1, 1, 1, 1, 12, 47, 47, 109, 47, 47, 141, 1, 1, 1, 1] 327 rigid atoms, others: [32, 1, 33, 19, 20, 21, 22, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 437 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: REAL250005042399 none O=C(N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O)C1(F)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 5, 15, 5, 5, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 327 conformations in input total number of sets (complete confs): 327 using faster count positions algorithm for large data unique positions, atoms: [78, 78, 32, 32, 32, 31, 9, 1, 9, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 78, 109, 109, 109, 78, 31, 31, 1, 32, 32, 96, 109, 109, 109, 109] 327 rigid atoms, others: [7, 9, 10, 11, 12, 13, 14, 26] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 401 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042399 none O=C(N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O)C1(F)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 5, 15, 5, 5, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 327 conformations in input total number of sets (complete confs): 327 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 1, 1, 1, 1, 1, 1, 6, 6, 31, 31, 31, 31, 31, 1, 1, 1, 1, 7, 47, 47, 47, 7, 1, 1, 32, 1, 1, 3, 47, 47, 47, 47] 327 rigid atoms, others: [2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 24, 25, 27, 28] set([0, 1, 33, 32, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 26, 29, 30, 31]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042399 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042399 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042399/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042399 Building REAL250005042400 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042400' /scratch/stefan/7921153/working/building/REAL250005042400 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042400 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042400/0 /scratch/stefan/7921153/working/building/REAL250005042400 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 509) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/509 `/scratch/stefan/7921153/working/3D/509' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=C(F)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O) `REAL250005042400.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042400/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042400 none CC=C(F)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 15, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 162 conformations in input total number of sets (complete confs): 162 using faster count positions algorithm for large data unique positions, atoms: [54, 54, 41, 54, 41, 41, 24, 24, 24, 23, 8, 1, 8, 1, 1, 1, 1, 1, 1, 23, 24, 24, 24, 54, 54, 54, 54, 41, 23, 23, 1, 23, 23, 72] 162 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33]) total number of confs: 216 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042400 none CC=C(F)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 15, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 162 conformations in input total number of sets (complete confs): 162 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 7, 24, 7, 7, 1, 1, 1, 1, 1, 1, 6, 6, 23, 23, 23, 23, 23, 1, 1, 1, 1, 24, 24, 24, 24, 7, 1, 1, 23, 1, 1, 3] 162 rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 28, 29, 31] set([0, 1, 2, 3, 4, 5, 33, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 30]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042400 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042400 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042400/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042400 Building REAL250005042401 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042401' /scratch/stefan/7921153/working/building/REAL250005042401 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042401 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042401/0 /scratch/stefan/7921153/working/building/REAL250005042401 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 510) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/510 `/scratch/stefan/7921153/working/3D/510' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CO)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O) `REAL250005042401.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042401/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:2-3 Rotatable hydrogens reported. Reducing confs by a factor of 3 WARNING:root:Setting energy window to 12 and max confs to 66 ('energy: ', 12.0) ('conf: ', 66) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042401 none CC(CO)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [67, 34, 67, 67, 34, 34, 15, 15, 15, 14, 5, 1, 5, 1, 1, 1, 1, 1, 1, 14, 15, 15, 15, 67, 67, 67, 67, 67, 67, 201, 34, 14, 15, 1, 14, 14, 45] 603 rigid atoms, others: [33, 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, 34, 35, 36]) total number of confs: 477 number of broken/clashed sets: 81 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042401 none CC(CO)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [32, 6, 32, 45, 6, 6, 1, 1, 1, 1, 1, 1, 5, 5, 15, 15, 15, 14, 14, 1, 1, 1, 1, 32, 32, 32, 32, 45, 45, 135, 6, 1, 1, 15, 1, 1, 6] 603 rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 33, 36]) total number of confs: 341 number of broken/clashed sets: 81 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042401 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042401 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042401/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042401 Building REAL250005042402 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042402' /scratch/stefan/7921153/working/building/REAL250005042402 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042402 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042402/0 /scratch/stefan/7921153/working/building/REAL250005042402 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 511) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/511 `/scratch/stefan/7921153/working/3D/511' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](O)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O) `REAL250005042402.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042402.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042402/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:2-3 Rotatable hydrogens reported. Reducing confs by a factor of 3 WARNING:root:Setting energy window to 12 and max confs to 66 ('energy: ', 12.0) ('conf: ', 66) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042402 none C[C@H](O)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 342 conformations in input total number of sets (complete confs): 342 using faster count positions algorithm for large data unique positions, atoms: [38, 28, 38, 38, 28, 28, 17, 17, 17, 16, 6, 1, 6, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 38, 38, 38, 114, 28, 16, 16, 1, 17, 17, 51] 342 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33]) total number of confs: 280 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042402 none C[C@H](O)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 342 conformations in input total number of sets (complete confs): 342 using faster count positions algorithm for large data unique positions, atoms: [25, 6, 25, 25, 6, 6, 1, 1, 1, 1, 1, 1, 5, 5, 16, 16, 16, 16, 16, 1, 1, 1, 1, 25, 25, 25, 75, 6, 1, 1, 17, 1, 1, 3] 342 rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 28, 29, 31] set([0, 1, 2, 3, 4, 5, 33, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 30]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042402 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042402 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042402/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042402 Building REAL250005042403 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042403' /scratch/stefan/7921153/working/building/REAL250005042403 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042403 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042403/0 /scratch/stefan/7921153/working/building/REAL250005042403 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 512) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/512 `/scratch/stefan/7921153/working/3D/512' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C1CC1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O) `REAL250005042403.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042403/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042403 none C=C1CC1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 393 conformations in input total number of sets (complete confs): 393 using faster count positions algorithm for large data unique positions, atoms: [131, 131, 131, 64, 64, 64, 27, 27, 27, 26, 9, 1, 9, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 131, 131, 131, 131, 131, 64, 26, 26, 1, 27, 27, 81] 393 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 31] 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, 32, 33, 34]) total number of confs: 444 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: REAL250005042403 none C=C1CC1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 393 conformations in input total number of sets (complete confs): 393 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 53, 7, 7, 7, 1, 1, 1, 1, 1, 1, 6, 6, 26, 26, 26, 26, 26, 1, 1, 1, 1, 53, 53, 53, 53, 53, 7, 1, 1, 26, 1, 1, 3] 393 rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 29, 30] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 34, 23, 24, 25, 26, 27, 28, 31]) total number of confs: 159 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042403 none C=C1CC1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 393 conformations in input total number of sets (complete confs): 393 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 13, 13, 13, 53, 53, 53, 53, 109, 109, 131, 131, 131, 131, 131, 53, 53, 53, 53, 1, 1, 1, 1, 1, 13, 53, 53, 131, 53, 53, 159] 393 rigid atoms, others: [0, 1, 2, 3, 4, 23, 24, 25, 26, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 515 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042403 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042403 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042403/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042403 Building REAL250005042404 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042404' /scratch/stefan/7921153/working/building/REAL250005042404 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042404 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042404/0 /scratch/stefan/7921153/working/building/REAL250005042404 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 513) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/513 `/scratch/stefan/7921153/working/3D/513' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C(C)CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O) `REAL250005042404.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042404/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042404 none C=C(C)CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 255 conformations in input total number of sets (complete confs): 255 using faster count positions algorithm for large data unique positions, atoms: [85, 85, 85, 34, 34, 34, 16, 16, 16, 16, 7, 1, 7, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 85, 85, 85, 85, 85, 85, 85, 34, 16, 16, 1, 16, 16, 48] 255 rigid atoms, others: [33, 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, 34, 35, 36]) total number of confs: 345 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042404 none C=C(C)CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 255 conformations in input total number of sets (complete confs): 255 using faster count positions algorithm for large data unique positions, atoms: [58, 45, 58, 6, 6, 6, 1, 1, 1, 1, 1, 1, 5, 5, 16, 16, 16, 16, 16, 1, 1, 1, 1, 58, 58, 58, 58, 58, 45, 45, 6, 1, 1, 16, 1, 1, 3] 255 rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 33, 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/7921153/working/building/REAL250005042404 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042404 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042404/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042404 Building REAL250005042405 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042405' /scratch/stefan/7921153/working/building/REAL250005042405 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042405 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042405/0 /scratch/stefan/7921153/working/building/REAL250005042405 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 514) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/514 `/scratch/stefan/7921153/working/3D/514' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O) `REAL250005042405.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042405.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042405/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042405 none CC=CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [67, 67, 53, 53, 53, 28, 28, 28, 28, 9, 1, 9, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 67, 67, 67, 67, 67, 53, 28, 28, 1, 28, 28, 84] 201 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33]) total number of confs: 270 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042405 none CC=CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 23, 6, 6, 6, 1, 1, 1, 1, 1, 1, 7, 7, 28, 28, 28, 28, 28, 1, 1, 1, 1, 23, 23, 23, 23, 23, 6, 1, 1, 28, 1, 1, 6] 201 rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 28, 29, 31] set([0, 1, 2, 3, 4, 33, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 30]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042405 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042405 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042405/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042405 Building REAL250005042406 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042406' /scratch/stefan/7921153/working/building/REAL250005042406 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042406 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042406/0 /scratch/stefan/7921153/working/building/REAL250005042406 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 515) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/515 `/scratch/stefan/7921153/working/3D/515' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H]1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O) `REAL250005042406.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042406.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042406/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042406 none C[C@@H]1C[C@H]1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 237 conformations in input total number of sets (complete confs): 237 using faster count positions algorithm for large data unique positions, atoms: [79, 79, 79, 79, 39, 79, 39, 39, 19, 19, 19, 18, 7, 1, 7, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 79, 79, 79, 79, 79, 39, 18, 18, 1, 19, 19, 57] 237 rigid atoms, others: [33, 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, 34, 35, 36]) total number of confs: 272 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: REAL250005042406 none C[C@@H]1C[C@H]1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 237 conformations in input total number of sets (complete confs): 237 using faster count positions algorithm for large data unique positions, atoms: [43, 43, 43, 43, 7, 43, 7, 7, 1, 1, 1, 1, 1, 1, 5, 5, 18, 18, 18, 18, 18, 1, 1, 1, 1, 43, 43, 43, 43, 43, 7, 1, 1, 19, 1, 1, 3] 237 rigid atoms, others: [32, 34, 35, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 33, 36]) total number of confs: 132 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042406 none C[C@@H]1C[C@H]1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 237 conformations in input total number of sets (complete confs): 237 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 43, 43, 43, 43, 76, 76, 79, 79, 79, 79, 79, 43, 43, 43, 43, 2, 2, 2, 1, 1, 12, 43, 43, 79, 43, 43, 129] 237 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 358 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042406 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042406 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042406/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042406 Building REAL250005042407 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042407' /scratch/stefan/7921153/working/building/REAL250005042407 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042407 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042407/0 /scratch/stefan/7921153/working/building/REAL250005042407 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 516) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/516 `/scratch/stefan/7921153/working/3D/516' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O)C1(O)CC1) `REAL250005042407.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042407.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042407/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:2-3 Rotatable hydrogens reported. Reducing confs by a factor of 3 WARNING:root:Setting energy window to 12 and max confs to 66 ('energy: ', 12.0) ('conf: ', 66) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042407 none O=C(N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O)C1(O)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 5, 12, 5, 5, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 468 conformations in input total number of sets (complete confs): 468 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 33, 33, 33, 33, 49, 49, 52, 52, 52, 52, 52, 33, 33, 33, 33, 1, 1, 1, 1, 12, 33, 33, 52, 33, 33, 99, 6, 1, 1, 1, 1] 468 rigid atoms, others: [32, 1, 34, 33, 19, 20, 21, 22, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 242 number of broken/clashed sets: 9 ./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: REAL250005042407 none O=C(N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O)C1(O)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 5, 12, 5, 5, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 468 conformations in input total number of sets (complete confs): 468 using faster count positions algorithm for large data unique positions, atoms: [39, 39, 19, 19, 19, 18, 6, 1, 6, 1, 1, 1, 1, 1, 1, 18, 19, 19, 19, 39, 52, 52, 52, 39, 18, 19, 1, 18, 18, 57, 156, 52, 52, 52, 52] 468 rigid atoms, others: [7, 9, 10, 11, 12, 13, 14, 26] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 356 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042407 none O=C(N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1O)C1(O)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 5, 12, 5, 5, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 468 conformations in input total number of sets (complete confs): 468 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 1, 1, 1, 1, 1, 1, 5, 5, 18, 18, 19, 18, 18, 1, 1, 1, 1, 7, 33, 33, 33, 7, 1, 1, 19, 1, 1, 6, 99, 33, 33, 33, 33] 468 rigid atoms, others: [2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 24, 25, 27, 28] set([0, 1, 34, 33, 32, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 26, 29, 30, 31]) total number of confs: 214 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042407 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042407 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042407/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042407 Building REAL250005042408 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042408' /scratch/stefan/7921153/working/building/REAL250005042408 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042408 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042408/0 /scratch/stefan/7921153/working/building/REAL250005042408 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 517) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/517 `/scratch/stefan/7921153/working/3D/517' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1CC1)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042408.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042408/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042408 none O=C(CC1CC1)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 183 conformations in input total number of sets (complete confs): 183 using faster count positions algorithm for large data unique positions, atoms: [36, 19, 36, 53, 61, 61, 19, 19, 19, 19, 19, 9, 19, 9, 1, 9, 1, 1, 1, 1, 1, 1, 19, 53, 53, 61, 61, 61, 61, 61, 19, 19, 57, 9, 1, 19, 19] 183 rigid atoms, others: [34, 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, 35, 36]) total number of confs: 269 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: REAL250005042408 none O=C(CC1CC1)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 183 conformations in input total number of sets (complete confs): 183 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 26, 35, 35, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 19, 19, 19, 19, 19, 1, 26, 26, 35, 35, 35, 35, 35, 1, 1, 6, 7, 19, 1, 1] 183 rigid atoms, others: [1, 35, 36, 6, 7, 8, 9, 10, 11, 12, 13, 22, 30, 31] set([0, 2, 3, 4, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34]) total number of confs: 162 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042408 none O=C(CC1CC1)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 183 conformations in input total number of sets (complete confs): 183 using faster count positions algorithm for large data unique positions, atoms: [16, 3, 1, 1, 1, 1, 16, 35, 35, 35, 35, 35, 35, 35, 57, 57, 57, 61, 61, 61, 61, 61, 35, 3, 3, 1, 1, 1, 1, 1, 35, 35, 105, 57, 61, 35, 35] 183 rigid atoms, others: [2, 3, 4, 5, 25, 26, 27, 28, 29] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 253 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042408 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042408 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042408/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042408 Building REAL250005042409 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042409' /scratch/stefan/7921153/working/building/REAL250005042409 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042409 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042409/0 /scratch/stefan/7921153/working/building/REAL250005042409 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 518) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/518 `/scratch/stefan/7921153/working/3D/518' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042409.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042409.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042409/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042409 none COCC(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 156 conformations in input total number of sets (complete confs): 156 using faster count positions algorithm for large data unique positions, atoms: [52, 52, 29, 16, 29, 16, 16, 16, 16, 16, 7, 16, 7, 1, 7, 1, 1, 1, 1, 1, 1, 16, 52, 52, 52, 52, 52, 16, 16, 48, 8, 1, 16, 16] 156 rigid atoms, others: [13, 15, 16, 17, 18, 19, 20, 31] 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, 32, 33]) total number of confs: 239 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042409 none COCC(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 156 conformations in input total number of sets (complete confs): 156 using faster count positions algorithm for large data unique positions, atoms: [33, 18, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 16, 16, 16, 16, 16, 1, 33, 33, 33, 18, 18, 1, 1, 6, 6, 16, 1, 1] 156 rigid atoms, others: [32, 33, 3, 5, 6, 7, 8, 9, 10, 11, 12, 21, 27, 28] set([0, 1, 2, 4, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 29, 30, 31]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042409 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042409 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042409/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042409 Building REAL250005042410 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042410' /scratch/stefan/7921153/working/building/REAL250005042410 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042410 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042410/0 /scratch/stefan/7921153/working/building/REAL250005042410 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 519) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/519 `/scratch/stefan/7921153/working/3D/519' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042410.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042410.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042410/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042410 none CCCC(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 153 conformations in input total number of sets (complete confs): 153 using faster count positions algorithm for large data unique positions, atoms: [51, 50, 26, 15, 26, 15, 15, 15, 15, 15, 7, 15, 7, 1, 7, 1, 1, 1, 1, 1, 1, 15, 51, 51, 51, 51, 51, 50, 50, 15, 15, 45, 7, 1, 15, 15] 153 rigid atoms, others: [33, 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, 34, 35]) total number of confs: 230 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042410 none CCCC(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 153 conformations in input total number of sets (complete confs): 153 using faster count positions algorithm for large data unique positions, atoms: [21, 17, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 15, 15, 15, 15, 15, 1, 22, 22, 22, 22, 22, 17, 17, 1, 1, 6, 6, 15, 1, 1] 153 rigid atoms, others: [34, 3, 5, 6, 7, 8, 9, 10, 11, 12, 35, 21, 29, 30] set([0, 1, 2, 4, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042410 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042410 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042410/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042410 Building REAL250005042411 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042411' /scratch/stefan/7921153/working/building/REAL250005042411 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042411 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042411/0 /scratch/stefan/7921153/working/building/REAL250005042411 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 520) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/520 `/scratch/stefan/7921153/working/3D/520' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042411.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042411.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042411/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042411 none CC(C)CC(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 30, 21, 11, 21, 11, 11, 11, 11, 11, 5, 11, 5, 1, 5, 1, 1, 1, 1, 1, 1, 11, 30, 30, 30, 30, 30, 30, 30, 30, 30, 11, 11, 33, 5, 1, 11, 11] 90 rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 140 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042411 none CC(C)CC(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [14, 14, 16, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 11, 11, 11, 11, 11, 1, 16, 16, 16, 16, 16, 16, 16, 14, 14, 1, 1, 6, 6, 11, 1, 1] 90 rigid atoms, others: [32, 33, 4, 37, 6, 7, 8, 9, 10, 11, 12, 13, 22, 38] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 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/7921153/working/building/REAL250005042411 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042411 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042411/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042411 Building REAL250005042412 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042412' /scratch/stefan/7921153/working/building/REAL250005042412 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042412 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042412/0 /scratch/stefan/7921153/working/building/REAL250005042412 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 521) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/521 `/scratch/stefan/7921153/working/3D/521' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC1C(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042412.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042412/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042412 none CC1CC1C(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [31, 31, 31, 23, 14, 23, 14, 14, 14, 14, 14, 7, 14, 7, 1, 7, 1, 1, 1, 1, 1, 1, 14, 31, 31, 31, 31, 31, 31, 31, 14, 14, 42, 7, 1, 14, 14] 93 rigid atoms, others: [34, 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, 35, 36]) total number of confs: 137 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: REAL250005042412 none CC1CC1C(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [16, 16, 16, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 14, 14, 14, 14, 14, 1, 16, 16, 16, 16, 16, 16, 16, 1, 1, 6, 6, 14, 1, 1] 93 rigid atoms, others: [35, 4, 6, 7, 8, 9, 10, 11, 12, 13, 22, 36, 30, 31] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34]) total number of confs: 71 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042412 none CC1CC1C(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 8, 8, 16, 16, 16, 16, 16, 16, 16, 27, 27, 27, 31, 31, 31, 31, 31, 16, 2, 2, 2, 1, 1, 1, 1, 16, 16, 48, 27, 31, 16, 16] 93 rigid atoms, others: [0, 1, 2, 3, 4, 26, 27, 28, 29] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042412 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042412 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042412/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042412 Building REAL250005042413 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042413' /scratch/stefan/7921153/working/building/REAL250005042413 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042413 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042413/0 /scratch/stefan/7921153/working/building/REAL250005042413 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 522) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/522 `/scratch/stefan/7921153/working/3D/522' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCC(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042413.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042413.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042413/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042413 none CCOCC(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 321 conformations in input total number of sets (complete confs): 321 using faster count positions algorithm for large data unique positions, atoms: [107, 105, 84, 40, 19, 40, 19, 19, 19, 19, 19, 9, 19, 9, 1, 9, 1, 1, 1, 1, 1, 1, 19, 107, 107, 107, 107, 107, 84, 84, 19, 19, 57, 9, 1, 19, 19] 321 rigid atoms, others: [34, 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, 35, 36]) total number of confs: 420 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042413 none CCOCC(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 321 conformations in input total number of sets (complete confs): 321 using faster count positions algorithm for large data unique positions, atoms: [64, 58, 25, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 19, 19, 19, 19, 19, 1, 65, 65, 65, 64, 64, 25, 25, 1, 1, 6, 7, 19, 1, 1] 321 rigid atoms, others: [35, 4, 6, 7, 8, 9, 10, 11, 12, 13, 22, 36, 30, 31] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34]) total number of confs: 210 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042413 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042413 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042413/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042413 Building REAL250005042414 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042414' /scratch/stefan/7921153/working/building/REAL250005042414 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042414 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042414/0 /scratch/stefan/7921153/working/building/REAL250005042414 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 523) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/523 `/scratch/stefan/7921153/working/3D/523' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)=CC(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042414.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042414.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042414/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042414 none CC(C)=CC(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 5, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [26, 26, 26, 17, 9, 17, 9, 9, 9, 9, 9, 5, 9, 5, 1, 5, 1, 1, 1, 1, 1, 1, 9, 26, 26, 26, 26, 26, 26, 26, 9, 9, 27, 5, 1, 9, 9] 78 rigid atoms, others: [34, 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, 35, 36]) total number of confs: 108 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042414 none CC(C)=CC(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 5, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [12, 12, 12, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 9, 9, 9, 9, 9, 1, 12, 12, 12, 12, 12, 12, 12, 1, 1, 6, 7, 9, 1, 1] 78 rigid atoms, others: [35, 4, 6, 7, 8, 9, 10, 11, 12, 13, 22, 36, 30, 31] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042414 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042414 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042414/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042414 Building REAL250005042415 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042415' /scratch/stefan/7921153/working/building/REAL250005042415 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042415 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042415/0 /scratch/stefan/7921153/working/building/REAL250005042415 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 524) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/524 `/scratch/stefan/7921153/working/3D/524' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCC(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042415.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042415.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042415/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042415 none CCCCC(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 258 conformations in input total number of sets (complete confs): 258 using faster count positions algorithm for large data unique positions, atoms: [86, 82, 73, 29, 15, 29, 15, 15, 15, 15, 15, 7, 15, 7, 1, 7, 1, 1, 1, 1, 1, 1, 15, 86, 86, 86, 86, 86, 82, 82, 73, 73, 15, 15, 45, 7, 1, 15, 15] 258 rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 387 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042415 none CCCCC(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 258 conformations in input total number of sets (complete confs): 258 using faster count positions algorithm for large data unique positions, atoms: [48, 31, 25, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 15, 15, 15, 15, 15, 1, 48, 48, 48, 46, 47, 33, 33, 25, 25, 1, 1, 6, 6, 15, 1, 1] 258 rigid atoms, others: [32, 33, 4, 37, 6, 7, 8, 9, 10, 11, 12, 13, 22, 38] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36]) total number of confs: 244 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042415 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042415 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042415/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042415 Building REAL250005042416 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042416' /scratch/stefan/7921153/working/building/REAL250005042416 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042416 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042416/0 /scratch/stefan/7921153/working/building/REAL250005042416 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 525) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/525 `/scratch/stefan/7921153/working/3D/525' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042416.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042416.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042416/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042416 none CC(C)C(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 10, 16, 10, 10, 10, 10, 10, 5, 10, 5, 1, 5, 1, 1, 1, 1, 1, 1, 10, 16, 16, 16, 16, 16, 16, 16, 10, 10, 30, 5, 1, 10, 10] 48 rigid atoms, others: [33, 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, 34, 35]) total number of confs: 73 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042416 none CC(C)C(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [8, 5, 8, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 10, 10, 10, 10, 10, 1, 8, 8, 8, 8, 8, 8, 8, 1, 1, 6, 6, 10, 1, 1] 48 rigid atoms, others: [34, 3, 5, 6, 7, 8, 9, 10, 11, 12, 35, 21, 29, 30] set([0, 1, 2, 4, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042416 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042416 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042416/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042416 Building REAL250005042417 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042417' /scratch/stefan/7921153/working/building/REAL250005042417 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042417 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042417/0 /scratch/stefan/7921153/working/building/REAL250005042417 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 526) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/526 `/scratch/stefan/7921153/working/3D/526' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)C(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042417.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042417.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042417/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042417 none CCC(C)C(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 25, 33, 11, 25, 11, 11, 11, 11, 11, 7, 11, 7, 1, 7, 1, 1, 1, 1, 1, 1, 11, 33, 33, 33, 33, 33, 33, 33, 33, 33, 11, 11, 33, 7, 1, 11, 11] 99 rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 146 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042417 none CCC(C)C(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [14, 12, 6, 12, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 11, 11, 11, 11, 11, 1, 15, 15, 15, 15, 15, 12, 12, 12, 12, 1, 1, 6, 6, 11, 1, 1] 99 rigid atoms, others: [32, 33, 4, 37, 6, 7, 8, 9, 10, 11, 12, 13, 22, 38] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042417 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042417 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042417/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042417 Building REAL250005042418 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042418' /scratch/stefan/7921153/working/building/REAL250005042418 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042418 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042418/0 /scratch/stefan/7921153/working/building/REAL250005042418 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 527) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/527 `/scratch/stefan/7921153/working/3D/527' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C)C(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042418.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042418.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042418/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042418 none COC(C)C(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [31, 31, 22, 31, 12, 22, 12, 12, 12, 12, 12, 7, 12, 7, 1, 7, 1, 1, 1, 1, 1, 1, 12, 31, 31, 31, 31, 31, 31, 31, 12, 12, 36, 7, 1, 12, 12] 93 rigid atoms, others: [34, 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, 35, 36]) total number of confs: 144 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042418 none COC(C)C(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [18, 14, 7, 14, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 12, 12, 12, 12, 12, 1, 18, 18, 18, 14, 14, 14, 14, 1, 1, 6, 7, 12, 1, 1] 93 rigid atoms, others: [35, 4, 6, 7, 8, 9, 10, 11, 12, 13, 22, 36, 30, 31] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34]) total number of confs: 83 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042418 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042418 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042418/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042418 Building REAL250005042419 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042419' /scratch/stefan/7921153/working/building/REAL250005042419 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042419 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042419/0 /scratch/stefan/7921153/working/building/REAL250005042419 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 528) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/528 `/scratch/stefan/7921153/working/3D/528' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCCC(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042419.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042419/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042419 none C=CCCC(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 267 conformations in input total number of sets (complete confs): 267 using faster count positions algorithm for large data unique positions, atoms: [89, 89, 79, 34, 17, 34, 17, 17, 17, 17, 17, 9, 17, 9, 1, 9, 1, 1, 1, 1, 1, 1, 17, 89, 89, 89, 89, 89, 79, 79, 17, 17, 51, 9, 1, 17, 17] 267 rigid atoms, others: [34, 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, 35, 36]) total number of confs: 395 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042419 none C=CCCC(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 267 conformations in input total number of sets (complete confs): 267 using faster count positions algorithm for large data unique positions, atoms: [58, 38, 27, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 17, 17, 17, 17, 17, 1, 58, 58, 58, 38, 38, 27, 27, 1, 1, 6, 6, 17, 1, 1] 267 rigid atoms, others: [35, 4, 6, 7, 8, 9, 10, 11, 12, 13, 22, 36, 30, 31] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34]) total number of confs: 258 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042419 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042419 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042419/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042419 Building REAL250005042420 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042420' /scratch/stefan/7921153/working/building/REAL250005042420 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042420 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042420/0 /scratch/stefan/7921153/working/building/REAL250005042420 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 529) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/529 `/scratch/stefan/7921153/working/3D/529' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C#N)C(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042420.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042420.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042420/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042420 none CC(C#N)C(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.1', 'N.1', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [23, 13, 23, 23, 10, 13, 10, 10, 10, 10, 10, 7, 10, 7, 1, 7, 1, 1, 1, 1, 1, 1, 10, 23, 23, 23, 23, 10, 10, 30, 7, 1, 10, 10] 69 rigid atoms, others: [14, 16, 17, 18, 19, 20, 21, 31] 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, 32, 33]) total number of confs: 125 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042420 none CC(C#N)C(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.1', 'N.1', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [9, 4, 9, 9, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 10, 10, 10, 10, 10, 1, 9, 9, 9, 9, 1, 1, 6, 6, 10, 1, 1] 69 rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 11, 12, 13, 22, 27, 28] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 29, 30, 31]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042420 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042420 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042420/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042420 Building REAL250005042421 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042421' /scratch/stefan/7921153/working/building/REAL250005042421 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042421 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042421/0 /scratch/stefan/7921153/working/building/REAL250005042421 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 530) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/530 `/scratch/stefan/7921153/working/3D/530' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=C(C)C(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042421.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042421/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042421 none CC=C(C)C(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [36, 36, 26, 36, 16, 26, 16, 16, 16, 16, 16, 10, 16, 10, 1, 10, 1, 1, 1, 1, 1, 1, 16, 36, 36, 36, 36, 36, 36, 36, 16, 16, 48, 10, 1, 16, 16] 108 rigid atoms, others: [34, 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, 35, 36]) total number of confs: 159 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042421 none CC=C(C)C(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [19, 19, 7, 19, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 16, 16, 16, 16, 16, 1, 19, 19, 19, 19, 19, 19, 19, 1, 1, 6, 6, 16, 1, 1] 108 rigid atoms, others: [35, 4, 6, 7, 8, 9, 10, 11, 12, 13, 22, 36, 30, 31] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042421 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042421 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042421/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042421 Building REAL250005042422 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042422' /scratch/stefan/7921153/working/building/REAL250005042422 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042422 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042422/0 /scratch/stefan/7921153/working/building/REAL250005042422 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 531) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/531 `/scratch/stefan/7921153/working/3D/531' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042422.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042422/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042422 none CCC(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [21, 20, 14, 20, 14, 14, 14, 14, 14, 7, 14, 7, 1, 7, 1, 1, 1, 1, 1, 1, 14, 21, 21, 21, 21, 21, 14, 14, 42, 7, 1, 14, 14] 63 rigid atoms, others: [12, 14, 15, 16, 17, 18, 19, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32]) total number of confs: 103 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042422 none CCC(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [11, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 14, 14, 14, 14, 14, 1, 11, 11, 11, 11, 11, 1, 1, 6, 6, 14, 1, 1] 63 rigid atoms, others: [32, 2, 4, 5, 6, 7, 8, 9, 10, 11, 20, 26, 27, 31] set([0, 1, 3, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 28, 29, 30]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042422 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042422 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042422/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042422 Building REAL250005042423 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042423' /scratch/stefan/7921153/working/building/REAL250005042423 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042423 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042423/0 /scratch/stefan/7921153/working/building/REAL250005042423 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 532) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/532 `/scratch/stefan/7921153/working/3D/532' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042423.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042423.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042423/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042423 none COCCC(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 243 conformations in input total number of sets (complete confs): 243 using faster count positions algorithm for large data unique positions, atoms: [81, 79, 69, 28, 16, 28, 16, 16, 16, 16, 16, 8, 16, 8, 1, 8, 1, 1, 1, 1, 1, 1, 16, 81, 81, 81, 79, 79, 69, 69, 16, 16, 48, 8, 1, 16, 16] 243 rigid atoms, others: [34, 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, 35, 36]) total number of confs: 356 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042423 none COCCC(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 243 conformations in input total number of sets (complete confs): 243 using faster count positions algorithm for large data unique positions, atoms: [53, 38, 26, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 16, 16, 16, 16, 16, 1, 53, 53, 53, 38, 38, 26, 26, 1, 1, 6, 6, 16, 1, 1] 243 rigid atoms, others: [35, 4, 6, 7, 8, 9, 10, 11, 12, 13, 22, 36, 30, 31] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042423 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042423 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042423/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042423 Building REAL250005042424 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042424' /scratch/stefan/7921153/working/building/REAL250005042424 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042424 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042424/0 /scratch/stefan/7921153/working/building/REAL250005042424 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 533) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/533 `/scratch/stefan/7921153/working/3D/533' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042424.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042424/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042424 none CC(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [10, 7, 10, 7, 7, 7, 7, 7, 4, 7, 4, 1, 4, 1, 1, 1, 1, 1, 1, 7, 10, 10, 10, 7, 7, 21, 4, 1, 7, 7] 30 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29]) total number of confs: 50 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042424 none CC(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 1, 2, 2, 2, 1, 1, 6, 5, 7, 1, 1] 30 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 19, 23, 24, 28, 29] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 25, 26, 27]) total number of confs: 24 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042424 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042424 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042424/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042424 Building REAL250005042425 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042425' /scratch/stefan/7921153/working/building/REAL250005042425 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042425 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042425/0 /scratch/stefan/7921153/working/building/REAL250005042425 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 534) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/534 `/scratch/stefan/7921153/working/3D/534' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CN(C(=O)C2CC2)C[C@H]1O)C1=CC(=O)[N-]O1) `REAL250005042425.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042425.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042425/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042425 none O=C(N[C@@H]1CN(C(=O)C2CC2)C[C@H]1O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 12, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 12, 12, 12, 12, 15, 15, 22, 22, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 6, 12, 12, 22, 22, 22, 22, 22, 12, 12, 36, 1] 66 rigid atoms, others: [1, 33, 16, 17, 18, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 105 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: REAL250005042425 none O=C(N[C@@H]1CN(C(=O)C2CC2)C[C@H]1O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 12, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 12, 12, 12, 12, 8, 1, 8, 1, 1, 1, 12, 12, 12, 12, 20, 22, 22, 22, 22, 22, 20, 12, 12, 1, 1, 1, 1, 1, 12, 12, 36, 22] 66 rigid atoms, others: [7, 9, 10, 11, 25, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 30, 31, 32, 33]) total number of confs: 89 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042425 none O=C(N[C@@H]1CN(C(=O)C2CC2)C[C@H]1O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 12, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 1, 4, 4, 12, 12, 1, 1, 1, 1, 6, 12, 12, 12, 12, 12, 6, 1, 1, 12, 12, 12, 12, 12, 1, 1, 6, 12] 66 rigid atoms, others: [2, 3, 4, 5, 6, 7, 12, 13, 14, 15, 23, 24, 30, 31] set([0, 1, 33, 32, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042425 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042425 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042425/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042425 Building REAL250005042426 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042426' /scratch/stefan/7921153/working/building/REAL250005042426 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042426 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042426/0 /scratch/stefan/7921153/working/building/REAL250005042426 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 535) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/535 `/scratch/stefan/7921153/working/3D/535' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CN(C(=O)C2CCC2)C[C@H]1O)C1=CC(=O)[N-]O1) `REAL250005042426.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042426.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042426/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042426 none O=C(N[C@@H]1CN(C(=O)C2CCC2)C[C@H]1O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 12, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [6, 1, 6, 6, 11, 11, 11, 11, 15, 15, 23, 23, 23, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 6, 11, 11, 23, 23, 23, 23, 23, 23, 23, 11, 11, 33, 1] 69 rigid atoms, others: [1, 36, 17, 18, 19, 20, 21, 22] set([0, 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]) total number of confs: 108 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: REAL250005042426 none O=C(N[C@@H]1CN(C(=O)C2CCC2)C[C@H]1O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 12, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [21, 21, 13, 13, 13, 13, 8, 1, 8, 1, 1, 1, 1, 13, 13, 13, 13, 21, 23, 23, 23, 23, 23, 21, 13, 13, 1, 1, 1, 1, 1, 1, 1, 13, 13, 39, 23] 69 rigid atoms, others: [32, 7, 9, 10, 11, 12, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 33, 34, 35, 36]) total number of confs: 93 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042426 none O=C(N[C@@H]1CN(C(=O)C2CCC2)C[C@H]1O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 12, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [6, 6, 1, 1, 1, 1, 1, 1, 5, 5, 13, 13, 13, 1, 1, 1, 1, 6, 11, 11, 11, 11, 11, 6, 1, 1, 13, 13, 13, 13, 13, 13, 13, 1, 1, 3, 11] 69 rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 13, 14, 15, 34, 24, 25, 16] set([0, 1, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 35, 36]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042426 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042426 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042426/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042426 Building REAL250005042427 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042427' /scratch/stefan/7921153/working/building/REAL250005042427 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042427 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042427/0 /scratch/stefan/7921153/working/building/REAL250005042427 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 536) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/536 `/scratch/stefan/7921153/working/3D/536' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042427.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042427.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042427/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042427 none NC(=O)C(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 6, 6, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [33, 23, 33, 14, 23, 14, 14, 14, 14, 14, 8, 14, 8, 1, 8, 1, 1, 1, 1, 1, 1, 14, 33, 33, 14, 14, 42, 8, 1, 14, 14] 99 rigid atoms, others: [13, 15, 16, 17, 18, 19, 20, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 29, 30]) total number of confs: 143 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042427 none NC(=O)C(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 6, 6, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [17, 5, 17, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 14, 14, 14, 14, 14, 1, 18, 18, 1, 1, 6, 7, 14, 1, 1] 99 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 11, 12, 21, 24, 25, 29, 30] set([0, 1, 2, 4, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 26, 27, 28]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042427 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042427 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042427/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042427 Building REAL250005042428 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042428' /scratch/stefan/7921153/working/building/REAL250005042428 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042428 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042428/0 /scratch/stefan/7921153/working/building/REAL250005042428 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 537) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/537 `/scratch/stefan/7921153/working/3D/537' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042428.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042428.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042428/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042428 none CC(C)(C)C(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 8, 12, 8, 8, 8, 8, 8, 5, 8, 5, 1, 5, 1, 1, 1, 1, 1, 1, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12, 8, 8, 24, 5, 1, 8, 8] 36 rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 59 number of broken/clashed sets: 36 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042428 none CC(C)(C)C(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 8, 8, 8, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 6, 5, 8, 1, 1] 36 rigid atoms, others: [32, 33, 4, 37, 6, 7, 8, 9, 10, 11, 12, 13, 22, 38] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36]) total number of confs: 27 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042428 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042428 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042428/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042428 Building REAL250005042429 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042429' /scratch/stefan/7921153/working/building/REAL250005042429 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042429 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042429/0 /scratch/stefan/7921153/working/building/REAL250005042429 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 538) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/538 `/scratch/stefan/7921153/working/3D/538' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C(=O)N2C[C@@H](O)[C@H](NC(=O)C3=CC(=O)[N-]O3)C2)CC1) `REAL250005042429.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042429.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042429/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042429 none CC1(C(=O)N2C[C@@H](O)[C@H](NC(=O)C3=CC(=O)[N-]O3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [18, 18, 8, 18, 8, 8, 8, 8, 8, 5, 8, 5, 1, 5, 1, 1, 1, 1, 1, 1, 8, 18, 18, 18, 18, 18, 8, 8, 24, 5, 1, 8, 8, 18, 18, 18, 18] 54 rigid atoms, others: [12, 14, 15, 16, 17, 18, 19, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36]) total number of confs: 69 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: REAL250005042429 none CC1(C(=O)N2C[C@@H](O)[C@H](NC(=O)C3=CC(=O)[N-]O3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [7, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 8, 8, 8, 8, 8, 1, 7, 7, 7, 7, 7, 1, 1, 6, 6, 8, 1, 1, 7, 7, 7, 7] 54 rigid atoms, others: [32, 2, 4, 5, 6, 7, 8, 9, 10, 11, 20, 26, 27, 31] set([0, 1, 3, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 28, 29, 30, 33, 34, 35, 36]) total number of confs: 38 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042429 none CC1(C(=O)N2C[C@@H](O)[C@H](NC(=O)C3=CC(=O)[N-]O3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 3, 3, 7, 7, 7, 7, 7, 7, 7, 17, 17, 17, 18, 18, 18, 18, 18, 7, 1, 1, 2, 2, 2, 7, 7, 21, 17, 18, 7, 7, 1, 1, 1, 1] 54 rigid atoms, others: [0, 1, 2, 35, 36, 33, 34, 21, 22] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042429 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042429 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042429/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042429 Building REAL250005042430 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042430' /scratch/stefan/7921153/working/building/REAL250005042430 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042430 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042430/0 /scratch/stefan/7921153/working/building/REAL250005042430 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 539) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/539 `/scratch/stefan/7921153/working/3D/539' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042430.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042430/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042430 none C[C@@H]1C[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [31, 31, 31, 31, 20, 31, 14, 20, 14, 14, 14, 14, 14, 7, 14, 7, 1, 7, 1, 1, 1, 1, 1, 1, 14, 31, 31, 31, 31, 31, 14, 14, 42, 7, 1, 14, 14] 93 rigid atoms, others: [34, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36]) total number of confs: 139 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: REAL250005042430 none C[C@@H]1C[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [16, 16, 16, 16, 6, 16, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 14, 14, 14, 14, 13, 1, 16, 16, 16, 16, 16, 1, 1, 6, 7, 14, 1, 1] 93 rigid atoms, others: [35, 36, 6, 8, 9, 10, 11, 12, 13, 14, 15, 24, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 32, 33, 34]) total number of confs: 72 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042430 none C[C@@H]1C[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 8, 8, 16, 16, 16, 16, 16, 16, 16, 27, 27, 27, 31, 31, 31, 31, 31, 16, 2, 2, 2, 1, 1, 16, 16, 48, 27, 31, 16, 16] 93 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042430 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042430 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042430/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042430 Building REAL250005042431 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042431' /scratch/stefan/7921153/working/building/REAL250005042431 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042431 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042431/0 /scratch/stefan/7921153/working/building/REAL250005042431 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 540) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/540 `/scratch/stefan/7921153/working/3D/540' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042431.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042431/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042431 none C[C@H]1C[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [31, 31, 31, 31, 23, 31, 14, 23, 14, 14, 14, 14, 14, 7, 14, 7, 1, 7, 1, 1, 1, 1, 1, 1, 14, 31, 31, 31, 31, 31, 14, 14, 42, 8, 1, 14, 14] 93 rigid atoms, others: [34, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36]) total number of confs: 139 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: REAL250005042431 none C[C@H]1C[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [16, 16, 16, 16, 5, 16, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 14, 14, 14, 14, 14, 1, 16, 16, 16, 16, 16, 1, 1, 6, 6, 14, 1, 1] 93 rigid atoms, others: [35, 36, 6, 8, 9, 10, 11, 12, 13, 14, 15, 24, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 32, 33, 34]) total number of confs: 71 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042431 none C[C@H]1C[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 8, 8, 16, 16, 16, 16, 16, 16, 16, 27, 27, 27, 31, 31, 31, 31, 31, 16, 2, 2, 2, 1, 1, 16, 16, 48, 27, 31, 16, 16] 93 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042431 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042431 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042431/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042431 Building REAL250005042432 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042432' /scratch/stefan/7921153/working/building/REAL250005042432 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042432 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042432/0 /scratch/stefan/7921153/working/building/REAL250005042432 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 541) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/541 `/scratch/stefan/7921153/working/3D/541' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CO)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042432.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042432.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042432/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:2-3 Rotatable hydrogens reported. Reducing confs by a factor of 3 WARNING:root:Setting energy window to 12 and max confs to 66 ('energy: ', 12.0) ('conf: ', 66) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042432 none O=C(CO)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 225 conformations in input total number of sets (complete confs): 225 using faster count positions algorithm for large data unique positions, atoms: [20, 14, 20, 25, 14, 14, 14, 14, 14, 8, 14, 8, 1, 8, 1, 1, 1, 1, 1, 1, 14, 25, 25, 75, 14, 14, 42, 8, 1, 14, 14] 225 rigid atoms, others: [12, 14, 15, 16, 17, 18, 19, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30]) total number of confs: 202 number of broken/clashed sets: 33 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042432 none O=C(CO)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 225 conformations in input total number of sets (complete confs): 225 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 11, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 14, 14, 14, 14, 14, 1, 11, 11, 33, 1, 1, 6, 7, 14, 1, 1] 225 rigid atoms, others: [1, 4, 5, 6, 7, 8, 9, 10, 11, 20, 24, 25, 29, 30] set([0, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 26, 27, 28]) total number of confs: 98 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042432 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042432 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042432/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042432 Building REAL250005042433 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042433' /scratch/stefan/7921153/working/building/REAL250005042433 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042433 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042433/0 /scratch/stefan/7921153/working/building/REAL250005042433 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 542) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/542 `/scratch/stefan/7921153/working/3D/542' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CN(C(=O)C2CCO2)C[C@H]1O)C1=CC(=O)[N-]O1) `REAL250005042433.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042433.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042433/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042433 none O=C(N[C@@H]1CN(C(=O)C2CCO2)C[C@H]1O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 7, 12, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 16, 16, 16, 16, 23, 23, 35, 35, 35, 16, 16, 16, 16, 1, 1, 1, 1, 1, 1, 8, 16, 16, 35, 35, 35, 35, 35, 16, 16, 48, 1] 105 rigid atoms, others: [1, 34, 17, 18, 19, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 153 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: REAL250005042433 none O=C(N[C@@H]1CN(C(=O)C2CCO2)C[C@H]1O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 7, 12, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 19, 19, 19, 19, 10, 1, 10, 1, 1, 1, 1, 19, 19, 19, 19, 32, 35, 35, 35, 35, 35, 32, 19, 19, 1, 1, 1, 1, 1, 19, 19, 57, 35] 105 rigid atoms, others: [7, 9, 10, 11, 12, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 31, 32, 33, 34]) total number of confs: 144 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042433 none O=C(N[C@@H]1CN(C(=O)C2CCO2)C[C@H]1O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 7, 12, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 1, 1, 1, 1, 1, 1, 5, 5, 19, 19, 19, 1, 1, 1, 1, 7, 16, 16, 16, 16, 16, 7, 1, 1, 19, 19, 19, 19, 19, 1, 1, 3, 16] 105 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 24, 25, 31] set([0, 1, 34, 33, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042433 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042433 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042433/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042433 Building REAL250005042434 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042434' /scratch/stefan/7921153/working/building/REAL250005042434 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042434 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042434/0 /scratch/stefan/7921153/working/building/REAL250005042434 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 543) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/543 `/scratch/stefan/7921153/working/3D/543' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CN(C(=O)C2COC2)C[C@H]1O)C1=CC(=O)[N-]O1) `REAL250005042434.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042434.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042434/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042434 none O=C(N[C@@H]1CN(C(=O)C2COC2)C[C@H]1O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 7, 12, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [5, 1, 5, 5, 12, 12, 12, 12, 16, 16, 24, 24, 24, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 5, 12, 12, 24, 24, 24, 24, 24, 12, 12, 36, 1] 72 rigid atoms, others: [1, 34, 17, 18, 19, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 113 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: REAL250005042434 none O=C(N[C@@H]1CN(C(=O)C2COC2)C[C@H]1O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 7, 12, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 13, 13, 13, 13, 8, 1, 8, 1, 1, 1, 1, 13, 13, 13, 13, 22, 24, 24, 24, 24, 24, 22, 13, 13, 1, 1, 1, 1, 1, 13, 13, 39, 24] 72 rigid atoms, others: [7, 9, 10, 11, 12, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 31, 32, 33, 34]) total number of confs: 95 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042434 none O=C(N[C@@H]1CN(C(=O)C2COC2)C[C@H]1O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 7, 12, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [7, 7, 1, 1, 1, 1, 1, 1, 5, 5, 13, 13, 13, 1, 1, 1, 1, 7, 12, 12, 12, 12, 12, 7, 1, 1, 13, 13, 13, 13, 13, 1, 1, 6, 12] 72 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 24, 25, 31] set([0, 1, 34, 33, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042434 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042434 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042434/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042434 Building REAL250005042435 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042435' /scratch/stefan/7921153/working/building/REAL250005042435 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042435 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042435/0 /scratch/stefan/7921153/working/building/REAL250005042435 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 544) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/544 `/scratch/stefan/7921153/working/3D/544' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(C=CCO)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042435.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042435.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042435/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:2-3 Rotatable hydrogens reported. Reducing confs by a factor of 3 WARNING:root:Setting energy window to 12 and max confs to 66 ('energy: ', 12.0) ('conf: ', 66) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042435 none O=C(C=CCO)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 1, 1, 5, 12, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 549 conformations in input total number of sets (complete confs): 549 using faster count positions algorithm for large data unique positions, atoms: [31, 17, 31, 58, 58, 61, 17, 17, 17, 17, 17, 9, 17, 9, 1, 9, 1, 1, 1, 1, 1, 1, 17, 58, 58, 61, 61, 183, 17, 17, 51, 9, 1, 17, 17] 549 rigid atoms, others: [32, 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, 33, 34]) total number of confs: 425 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042435 none O=C(C=CCO)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 1, 1, 5, 12, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 549 conformations in input total number of sets (complete confs): 549 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 21, 21, 44, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 17, 17, 17, 17, 17, 1, 21, 21, 44, 44, 132, 1, 1, 6, 6, 17, 1, 1] 549 rigid atoms, others: [1, 34, 33, 6, 7, 8, 9, 10, 11, 12, 13, 22, 28, 29] set([0, 32, 2, 3, 4, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 30, 31]) total number of confs: 326 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042435 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042435 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042435/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042435 Building REAL250005042436 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042436' /scratch/stefan/7921153/working/building/REAL250005042436 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042436 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042436/0 /scratch/stefan/7921153/working/building/REAL250005042436 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 545) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/545 `/scratch/stefan/7921153/working/3D/545' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC=CC(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042436.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042436.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042436/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042436 none CCC=CC(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [60, 47, 47, 30, 16, 30, 16, 16, 16, 16, 16, 9, 16, 9, 1, 9, 1, 1, 1, 1, 1, 1, 16, 60, 60, 60, 60, 60, 47, 47, 16, 16, 48, 9, 1, 16, 16] 180 rigid atoms, others: [34, 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, 35, 36]) total number of confs: 265 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042436 none CCC=CC(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [40, 25, 25, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 16, 16, 16, 16, 16, 1, 40, 40, 40, 40, 40, 25, 25, 1, 1, 6, 6, 16, 1, 1] 180 rigid atoms, others: [35, 4, 6, 7, 8, 9, 10, 11, 12, 13, 22, 36, 30, 31] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042436 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042436 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042436/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042436 Building REAL250005042437 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042437' /scratch/stefan/7921153/working/building/REAL250005042437 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042437 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042437/0 /scratch/stefan/7921153/working/building/REAL250005042437 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 546) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/546 `/scratch/stefan/7921153/working/3D/546' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCC(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042437.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042437.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042437/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042437 none C#CCCC(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 183 conformations in input total number of sets (complete confs): 183 using faster count positions algorithm for large data unique positions, atoms: [61, 61, 55, 28, 17, 28, 17, 17, 17, 17, 17, 7, 17, 7, 1, 7, 1, 1, 1, 1, 1, 1, 17, 61, 61, 61, 55, 55, 17, 17, 51, 7, 1, 17, 17] 183 rigid atoms, others: [32, 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, 33, 34]) total number of confs: 274 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042437 none C#CCCC(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 183 conformations in input total number of sets (complete confs): 183 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 19, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 17, 17, 17, 17, 17, 1, 30, 30, 30, 19, 19, 1, 1, 6, 6, 17, 1, 1] 183 rigid atoms, others: [33, 34, 4, 6, 7, 8, 9, 10, 11, 12, 13, 22, 28, 29] set([0, 1, 2, 3, 5, 32, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 30, 31]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042437 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042437 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042437/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042437 Building REAL250005042438 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042438' /scratch/stefan/7921153/working/building/REAL250005042438 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042438 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042438/0 /scratch/stefan/7921153/working/building/REAL250005042438 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 547) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/547 `/scratch/stefan/7921153/working/3D/547' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(O)C(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042438.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042438/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:2-3 Rotatable hydrogens reported. Reducing confs by a factor of 3 WARNING:root:Setting energy window to 12 and max confs to 66 ('energy: ', 12.0) ('conf: ', 66) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042438 none C=CC(O)C(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 504 conformations in input total number of sets (complete confs): 504 using faster count positions algorithm for large data unique positions, atoms: [56, 56, 33, 56, 15, 33, 15, 15, 15, 15, 15, 7, 15, 7, 1, 7, 1, 1, 1, 1, 1, 1, 15, 56, 56, 56, 56, 168, 15, 15, 45, 7, 1, 15, 15] 504 rigid atoms, others: [32, 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, 33, 34]) total number of confs: 410 number of broken/clashed sets: 36 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042438 none C=CC(O)C(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 504 conformations in input total number of sets (complete confs): 504 using faster count positions algorithm for large data unique positions, atoms: [35, 23, 7, 23, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 15, 15, 15, 15, 15, 1, 35, 35, 35, 23, 69, 1, 1, 6, 6, 15, 1, 1] 504 rigid atoms, others: [33, 34, 4, 6, 7, 8, 9, 10, 11, 12, 13, 22, 28, 29] set([0, 1, 2, 3, 5, 32, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 30, 31]) total number of confs: 226 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042438 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042438 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042438/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042438 Building REAL250005042439 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042439' /scratch/stefan/7921153/working/building/REAL250005042439 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042439 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042439/0 /scratch/stefan/7921153/working/building/REAL250005042439 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 548) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/548 `/scratch/stefan/7921153/working/3D/548' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)C(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042439.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042439.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042439/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:2-3 Rotatable hydrogens reported. Reducing confs by a factor of 3 WARNING:root:Setting energy window to 12 and max confs to 66 ('energy: ', 12.0) ('conf: ', 66) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042439 none CC(O)C(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 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: [22, 13, 22, 10, 13, 10, 10, 10, 10, 10, 6, 10, 6, 1, 6, 1, 1, 1, 1, 1, 1, 10, 22, 22, 22, 22, 66, 10, 10, 30, 6, 1, 10, 10] 198 rigid atoms, others: [13, 15, 16, 17, 18, 19, 20, 31] 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, 32, 33]) total number of confs: 176 number of broken/clashed sets: 30 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042439 none CC(O)C(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 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: [10, 4, 10, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 10, 10, 10, 10, 10, 1, 10, 10, 10, 10, 30, 1, 1, 6, 6, 10, 1, 1] 198 rigid atoms, others: [32, 33, 3, 5, 6, 7, 8, 9, 10, 11, 12, 21, 27, 28] set([0, 1, 2, 4, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 29, 30, 31]) total number of confs: 90 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042439 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042439 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042439/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042439 Building REAL250005042440 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042440' /scratch/stefan/7921153/working/building/REAL250005042440 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042440 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042440/0 /scratch/stefan/7921153/working/building/REAL250005042440 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 549) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/549 `/scratch/stefan/7921153/working/3D/549' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)C(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042440.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042440.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042440/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042440 none CC(=O)C(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 84 conformations in input total number of sets (complete confs): 84 using faster count positions algorithm for large data unique positions, atoms: [28, 19, 28, 14, 19, 14, 14, 14, 14, 14, 8, 14, 8, 1, 8, 1, 1, 1, 1, 1, 1, 14, 28, 28, 28, 14, 14, 42, 8, 1, 14, 14] 84 rigid atoms, others: [13, 15, 16, 17, 18, 19, 20, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31]) total number of confs: 129 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042440 none CC(=O)C(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 84 conformations in input total number of sets (complete confs): 84 using faster count positions algorithm for large data unique positions, atoms: [16, 5, 16, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 14, 14, 14, 14, 14, 1, 17, 17, 17, 1, 1, 6, 7, 14, 1, 1] 84 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 11, 12, 21, 25, 26, 30, 31] set([0, 1, 2, 4, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 27, 28, 29]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042440 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042440 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042440/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042440 Building REAL250005042441 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042441' /scratch/stefan/7921153/working/building/REAL250005042441 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042441 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042441/0 /scratch/stefan/7921153/working/building/REAL250005042441 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 550) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/550 `/scratch/stefan/7921153/working/3D/550' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CN(C(=O)C2(F)CC2)C[C@H]1O)C1=CC(=O)[N-]O1) `REAL250005042441.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042441/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042441 none O=C(N[C@@H]1CN(C(=O)C2(F)CC2)C[C@H]1O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 5, 15, 5, 5, 5, 5, 7, 12, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 84 conformations in input total number of sets (complete confs): 84 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 14, 14, 14, 14, 21, 21, 28, 28, 28, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 7, 14, 14, 28, 28, 28, 28, 14, 14, 42, 1] 84 rigid atoms, others: [1, 33, 17, 18, 19, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 131 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: REAL250005042441 none O=C(N[C@@H]1CN(C(=O)C2(F)CC2)C[C@H]1O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 5, 15, 5, 5, 5, 5, 7, 12, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 84 conformations in input total number of sets (complete confs): 84 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 12, 12, 12, 12, 6, 1, 6, 1, 1, 1, 1, 12, 12, 12, 12, 25, 28, 28, 28, 28, 28, 25, 12, 12, 1, 1, 1, 1, 12, 12, 36, 28] 84 rigid atoms, others: [7, 9, 10, 11, 12, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33]) total number of confs: 104 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042441 none O=C(N[C@@H]1CN(C(=O)C2(F)CC2)C[C@H]1O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 5, 15, 5, 5, 5, 5, 7, 12, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 84 conformations in input total number of sets (complete confs): 84 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 1, 1, 1, 1, 1, 1, 4, 4, 12, 12, 12, 1, 1, 1, 1, 7, 14, 14, 14, 14, 14, 7, 1, 1, 12, 12, 12, 12, 1, 1, 3, 14] 84 rigid atoms, others: [2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 24, 25, 30, 31] set([0, 1, 33, 32, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042441 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042441 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042441/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042441 Building REAL250005042442 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042442' /scratch/stefan/7921153/working/building/REAL250005042442 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042442 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042442/0 /scratch/stefan/7921153/working/building/REAL250005042442 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 551) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/551 `/scratch/stefan/7921153/working/3D/551' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=C(F)C(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042442.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042442.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042442/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042442 none CC=C(F)C(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 15, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 19, 30, 11, 19, 11, 11, 11, 11, 11, 5, 11, 5, 1, 5, 1, 1, 1, 1, 1, 1, 11, 30, 30, 30, 30, 11, 11, 33, 5, 1, 11, 11] 90 rigid atoms, others: [14, 16, 17, 18, 19, 20, 21, 31] 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, 32, 33]) total number of confs: 126 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042442 none CC=C(F)C(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 15, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 6, 17, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 11, 11, 11, 11, 11, 1, 18, 18, 18, 17, 1, 1, 6, 6, 11, 1, 1] 90 rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 11, 12, 13, 22, 27, 28] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 29, 30, 31]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042442 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042442 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042442/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042442 Building REAL250005042443 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042443' /scratch/stefan/7921153/working/building/REAL250005042443 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042443 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042443/0 /scratch/stefan/7921153/working/building/REAL250005042443 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 552) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/552 `/scratch/stefan/7921153/working/3D/552' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CO)C(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042443.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042443.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042443/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:2-3 Rotatable hydrogens reported. Reducing confs by a factor of 3 WARNING:root:Setting energy window to 12 and max confs to 66 ('energy: ', 12.0) ('conf: ', 66) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042443 none CC(CO)C(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 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: [18, 12, 18, 22, 8, 12, 8, 8, 8, 8, 8, 4, 8, 4, 1, 4, 1, 1, 1, 1, 1, 1, 8, 18, 18, 18, 18, 22, 22, 66, 8, 8, 24, 4, 1, 8, 8] 198 rigid atoms, others: [34, 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, 35, 36]) total number of confs: 183 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042443 none CC(CO)C(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 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: [7, 4, 7, 14, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 8, 8, 8, 8, 8, 1, 7, 7, 7, 7, 14, 14, 42, 1, 1, 6, 6, 8, 1, 1] 198 rigid atoms, others: [35, 4, 6, 7, 8, 9, 10, 11, 12, 13, 22, 36, 30, 31] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34]) total number of confs: 117 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042443 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042443 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042443/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042443 Building REAL250005042444 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042444' /scratch/stefan/7921153/working/building/REAL250005042444 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042444 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042444/0 /scratch/stefan/7921153/working/building/REAL250005042444 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 553) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/553 `/scratch/stefan/7921153/working/3D/553' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CN(C(=O)C2(O)CC2)C[C@H]1O)C1=CC(=O)[N-]O1) `REAL250005042444.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042444.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042444/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:2-3 Rotatable hydrogens reported. Reducing confs by a factor of 3 WARNING:root:Setting energy window to 12 and max confs to 66 ('energy: ', 12.0) ('conf: ', 66) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042444 none O=C(N[C@@H]1CN(C(=O)C2(O)CC2)C[C@H]1O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 12, 1, 1, 1, 11, 8, 12, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 207 conformations in input total number of sets (complete confs): 207 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 10, 10, 10, 10, 15, 15, 23, 23, 23, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 6, 10, 10, 69, 23, 23, 23, 23, 10, 10, 30, 1] 207 rigid atoms, others: [1, 34, 17, 18, 19, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 170 number of broken/clashed sets: 39 ./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: REAL250005042444 none O=C(N[C@@H]1CN(C(=O)C2(O)CC2)C[C@H]1O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 12, 1, 1, 1, 11, 8, 12, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 207 conformations in input total number of sets (complete confs): 207 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 10, 10, 10, 10, 6, 1, 6, 1, 1, 1, 1, 10, 10, 10, 10, 20, 23, 23, 23, 23, 23, 20, 10, 10, 6, 1, 1, 1, 1, 10, 10, 30, 23] 207 rigid atoms, others: [7, 9, 10, 11, 12, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34]) total number of confs: 95 number of broken/clashed sets: 39 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042444 none O=C(N[C@@H]1CN(C(=O)C2(O)CC2)C[C@H]1O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 12, 1, 1, 1, 11, 8, 12, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 207 conformations in input total number of sets (complete confs): 207 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 1, 5, 5, 10, 10, 10, 1, 1, 1, 1, 6, 10, 10, 10, 10, 10, 6, 1, 1, 30, 10, 10, 10, 10, 1, 1, 6, 10] 207 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 24, 25, 31] set([0, 1, 34, 33, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30]) total number of confs: 78 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042444 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042444 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042444/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042444 Building REAL250005042445 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042445' /scratch/stefan/7921153/working/building/REAL250005042445 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042445 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042445/0 /scratch/stefan/7921153/working/building/REAL250005042445 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 554) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/554 `/scratch/stefan/7921153/working/3D/554' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CN(C(=O)C2=CCC2)C[C@H]1O)C1=CC(=O)[N-]O1) `REAL250005042445.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042445/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042445 none O=C(N[C@@H]1CN(C(=O)C2=CCC2)C[C@H]1O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 7, 12, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [4, 1, 4, 4, 11, 11, 11, 11, 19, 19, 19, 19, 19, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 4, 11, 11, 19, 19, 19, 19, 19, 11, 11, 33, 1] 57 rigid atoms, others: [1, 34, 17, 18, 19, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 90 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: REAL250005042445 none O=C(N[C@@H]1CN(C(=O)C2=CCC2)C[C@H]1O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 7, 12, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [18, 18, 9, 9, 9, 9, 6, 1, 6, 1, 1, 1, 1, 9, 9, 9, 9, 18, 19, 19, 19, 19, 19, 18, 9, 9, 1, 1, 1, 1, 1, 9, 9, 27, 19] 57 rigid atoms, others: [7, 9, 10, 11, 12, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 31, 32, 33, 34]) total number of confs: 76 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042445 none O=C(N[C@@H]1CN(C(=O)C2=CCC2)C[C@H]1O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 7, 12, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [6, 6, 1, 1, 1, 1, 1, 1, 7, 7, 9, 9, 9, 1, 1, 1, 1, 6, 11, 11, 11, 11, 11, 6, 1, 1, 9, 9, 9, 9, 9, 1, 1, 6, 11] 57 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 24, 25, 31] set([0, 1, 34, 33, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042445 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042445 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042445/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042445 Building REAL250005042446 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042446' /scratch/stefan/7921153/working/building/REAL250005042446 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042446 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042446/0 /scratch/stefan/7921153/working/building/REAL250005042446 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 555) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/555 `/scratch/stefan/7921153/working/3D/555' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=CC(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042446.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042446.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042446/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042446 none CC=CC(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [24, 24, 17, 12, 17, 12, 12, 12, 12, 12, 7, 12, 7, 1, 7, 1, 1, 1, 1, 1, 1, 12, 24, 24, 24, 24, 24, 12, 12, 36, 7, 1, 12, 12] 72 rigid atoms, others: [13, 15, 16, 17, 18, 19, 20, 31] 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, 32, 33]) total number of confs: 109 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042446 none CC=CC(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [15, 15, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 12, 12, 1, 15, 15, 15, 15, 15, 1, 1, 6, 6, 12, 1, 1] 72 rigid atoms, others: [32, 33, 3, 5, 6, 7, 8, 9, 10, 11, 12, 21, 27, 28] set([0, 1, 2, 4, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 29, 30, 31]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042446 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042446 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042446/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042446 Building REAL250005042447 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042447' /scratch/stefan/7921153/working/building/REAL250005042447 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042447 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042447/0 /scratch/stefan/7921153/working/building/REAL250005042447 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 556) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/556 `/scratch/stefan/7921153/working/3D/556' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(C=CCF)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042447.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042447.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042447/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042447 none O=C(C=CCF)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 1, 1, 5, 15, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [20, 12, 20, 31, 31, 31, 12, 12, 12, 12, 12, 7, 12, 7, 1, 7, 1, 1, 1, 1, 1, 1, 12, 31, 31, 31, 31, 12, 12, 36, 7, 1, 12, 12] 93 rigid atoms, others: [14, 16, 17, 18, 19, 20, 21, 31] 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, 32, 33]) total number of confs: 129 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042447 none O=C(C=CCF)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 1, 1, 5, 15, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [4, 1, 4, 12, 12, 22, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 12, 12, 1, 12, 12, 22, 22, 1, 1, 6, 6, 12, 1, 1] 93 rigid atoms, others: [32, 1, 33, 6, 7, 8, 9, 10, 11, 12, 13, 22, 27, 28] set([0, 2, 3, 4, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 29, 30, 31]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042447 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042447 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042447/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042447 Building REAL250005042448 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042448' /scratch/stefan/7921153/working/building/REAL250005042448 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types Protomer extracton resulted in 0 protomers Marking REAL250005042448 as failed and skipping /scratch/stefan/7921153/working /scratch/stefan/7921153 `/scratch/stefan/7921153/working/building/REAL250005042448' -> `/scratch/stefan/7921153/failed/REAL250005042448' Building REAL250005042449 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042449' /scratch/stefan/7921153/working/building/REAL250005042449 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042449 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042449/0 /scratch/stefan/7921153/working/building/REAL250005042449 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 557) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/557 `/scratch/stefan/7921153/working/3D/557' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](O)C(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042449.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042449.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042449/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:2-3 Rotatable hydrogens reported. Reducing confs by a factor of 3 WARNING:root:Setting energy window to 12 and max confs to 66 ('energy: ', 12.0) ('conf: ', 66) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042449 none C[C@H](O)C(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 225 conformations in input total number of sets (complete confs): 225 using faster count positions algorithm for large data unique positions, atoms: [25, 15, 25, 25, 11, 15, 11, 11, 11, 11, 11, 5, 11, 5, 1, 5, 1, 1, 1, 1, 1, 1, 11, 25, 25, 25, 75, 11, 11, 33, 5, 1, 11, 11] 225 rigid atoms, others: [14, 16, 17, 18, 19, 20, 21, 31] 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, 32, 33]) total number of confs: 197 number of broken/clashed sets: 54 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042449 none C[C@H](O)C(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 225 conformations in input total number of sets (complete confs): 225 using faster count positions algorithm for large data unique positions, atoms: [9, 4, 9, 9, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 11, 11, 11, 11, 11, 1, 9, 9, 9, 27, 1, 1, 6, 7, 11, 1, 1] 225 rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 11, 12, 13, 22, 27, 28] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 29, 30, 31]) total number of confs: 82 number of broken/clashed sets: 54 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042449 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042449 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042449/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042449 Building REAL250005042450 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042450' /scratch/stefan/7921153/working/building/REAL250005042450 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042450 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042450/0 /scratch/stefan/7921153/working/building/REAL250005042450 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 558) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/558 `/scratch/stefan/7921153/working/3D/558' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CON=CC(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042450.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042450.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042450/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042450 none CON=CC(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 8, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 153 conformations in input total number of sets (complete confs): 153 using faster count positions algorithm for large data unique positions, atoms: [51, 51, 51, 29, 14, 29, 14, 14, 14, 14, 14, 8, 14, 8, 1, 8, 1, 1, 1, 1, 1, 1, 14, 51, 51, 51, 51, 14, 14, 42, 8, 1, 14, 14] 153 rigid atoms, others: [14, 16, 17, 18, 19, 20, 21, 31] 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, 32, 33]) total number of confs: 193 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042450 none CON=CC(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 8, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 153 conformations in input total number of sets (complete confs): 153 using faster count positions algorithm for large data unique positions, atoms: [31, 26, 26, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 14, 14, 14, 14, 14, 1, 31, 31, 31, 26, 1, 1, 6, 6, 14, 1, 1] 153 rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 11, 12, 13, 22, 27, 28] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 29, 30, 31]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042450 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042450 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042450/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042450 Building REAL250005042451 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042451' /scratch/stefan/7921153/working/building/REAL250005042451 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042451 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042451/0 /scratch/stefan/7921153/working/building/REAL250005042451 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 559) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/559 `/scratch/stefan/7921153/working/3D/559' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042451.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042451.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042451/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042451 none C[C@@H]1C[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [31, 31, 31, 31, 20, 31, 14, 20, 14, 14, 14, 14, 14, 7, 14, 7, 1, 7, 1, 1, 1, 1, 1, 1, 14, 31, 31, 31, 31, 31, 14, 14, 42, 7, 1, 14, 14] 93 rigid atoms, others: [34, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36]) total number of confs: 139 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: REAL250005042451 none C[C@@H]1C[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [16, 16, 16, 16, 6, 16, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 14, 14, 14, 14, 13, 1, 16, 16, 16, 16, 16, 1, 1, 6, 7, 14, 1, 1] 93 rigid atoms, others: [35, 36, 6, 8, 9, 10, 11, 12, 13, 14, 15, 24, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 32, 33, 34]) total number of confs: 72 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042451 none C[C@@H]1C[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 8, 8, 16, 16, 16, 16, 16, 16, 16, 27, 27, 27, 31, 31, 31, 31, 31, 16, 2, 2, 2, 1, 1, 16, 16, 48, 27, 31, 16, 16] 93 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042451 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042451 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042451/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042451 Building REAL250005042452 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042452' /scratch/stefan/7921153/working/building/REAL250005042452 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042452 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042452/0 /scratch/stefan/7921153/working/building/REAL250005042452 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 560) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/560 `/scratch/stefan/7921153/working/3D/560' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(O)C(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042452.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042452/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:2-3 Rotatable hydrogens reported. Reducing confs by a factor of 3 WARNING:root:Setting energy window to 12 and max confs to 66 ('energy: ', 12.0) ('conf: ', 66) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042452 none CC(C)(O)C(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 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: [21, 17, 21, 21, 11, 17, 11, 11, 11, 11, 11, 5, 11, 5, 1, 5, 1, 1, 1, 1, 1, 1, 11, 21, 21, 21, 21, 21, 21, 63, 11, 11, 33, 6, 1, 11, 11] 189 rigid atoms, others: [34, 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, 35, 36]) total number of confs: 165 number of broken/clashed sets: 63 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042452 none CC(C)(O)C(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 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: [9, 5, 9, 9, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 11, 11, 11, 11, 11, 1, 9, 9, 9, 9, 9, 9, 27, 1, 1, 6, 7, 11, 1, 1] 189 rigid atoms, others: [35, 4, 6, 7, 8, 9, 10, 11, 12, 13, 22, 36, 30, 31] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34]) total number of confs: 85 number of broken/clashed sets: 63 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042452 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042452 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042452/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042452 Building REAL250005042453 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042453' /scratch/stefan/7921153/working/building/REAL250005042453 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042453 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042453/0 /scratch/stefan/7921153/working/building/REAL250005042453 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 561) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/561 `/scratch/stefan/7921153/working/3D/561' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C(C)CC(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042453.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042453.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042453/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042453 none C=C(C)CC(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [58, 58, 58, 25, 14, 25, 14, 14, 14, 14, 14, 7, 14, 7, 1, 7, 1, 1, 1, 1, 1, 1, 14, 58, 58, 58, 58, 58, 58, 58, 14, 14, 42, 7, 1, 14, 14] 174 rigid atoms, others: [34, 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, 35, 36]) total number of confs: 257 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042453 none C=C(C)CC(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [36, 27, 36, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 14, 14, 14, 14, 14, 1, 36, 36, 36, 36, 36, 27, 27, 1, 1, 6, 6, 14, 1, 1] 174 rigid atoms, others: [35, 4, 6, 7, 8, 9, 10, 11, 12, 13, 22, 36, 30, 31] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042453 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042453 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042453/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042453 Building REAL250005042454 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042454' /scratch/stefan/7921153/working/building/REAL250005042454 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042454 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042454/0 /scratch/stefan/7921153/working/building/REAL250005042454 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 562) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/562 `/scratch/stefan/7921153/working/3D/562' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042454.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042454/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042454 none C=CCC(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [50, 50, 29, 15, 29, 15, 15, 15, 15, 15, 7, 15, 7, 1, 7, 1, 1, 1, 1, 1, 1, 15, 50, 50, 50, 50, 50, 15, 15, 45, 7, 1, 15, 15] 150 rigid atoms, others: [13, 15, 16, 17, 18, 19, 20, 31] 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, 32, 33]) total number of confs: 228 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042454 none C=CCC(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [34, 19, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 15, 15, 15, 15, 15, 1, 34, 34, 34, 19, 19, 1, 1, 6, 6, 15, 1, 1] 150 rigid atoms, others: [32, 33, 3, 5, 6, 7, 8, 9, 10, 11, 12, 21, 27, 28] set([0, 1, 2, 4, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 29, 30, 31]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042454 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042454 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042454/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042454 Building REAL250005042455 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042455' /scratch/stefan/7921153/working/building/REAL250005042455 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005042455 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042455/0 /scratch/stefan/7921153/working/building/REAL250005042455 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 563) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/563 `/scratch/stefan/7921153/working/3D/563' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[NH+](C)CC(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042455.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042455.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042455/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042455 none C[NH+](C)CC(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [31, 31, 31, 31, 26, 15, 26, 15, 15, 15, 15, 15, 8, 15, 8, 1, 8, 1, 1, 1, 1, 1, 1, 15, 31, 31, 31, 31, 31, 31, 31, 31, 15, 15, 45, 8, 1, 15, 15] 93 rigid atoms, others: [36, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 145 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042455 none C[NH+](C)CC(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [21, 20, 21, 21, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 15, 15, 15, 15, 15, 1, 21, 21, 21, 21, 21, 21, 20, 20, 1, 1, 6, 5, 15, 1, 1] 93 rigid atoms, others: [32, 33, 5, 38, 7, 8, 9, 10, 11, 12, 13, 14, 23, 37] set([0, 1, 2, 3, 4, 6, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042455 /scratch/stefan/7921153/working /scratch/stefan/7921153 mkdir: created directory `1' /scratch/stefan/7921153/working/building/REAL250005042455/1 /scratch/stefan/7921153/working/building/REAL250005042455 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 1 (index: 564) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/564 `/scratch/stefan/7921153/working/3D/564' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CC(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042455.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005042455.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042455/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042455 none CN(C)CC(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 156 conformations in input total number of sets (complete confs): 156 using faster count positions algorithm for large data unique positions, atoms: [52, 52, 52, 30, 11, 30, 11, 11, 11, 11, 11, 3, 11, 3, 1, 3, 1, 1, 1, 1, 1, 1, 11, 52, 52, 52, 52, 52, 52, 52, 52, 11, 11, 33, 3, 1, 11, 11] 156 rigid atoms, others: [35, 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, 36, 37]) total number of confs: 210 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042455 none CN(C)CC(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 156 conformations in input total number of sets (complete confs): 156 using faster count positions algorithm for large data unique positions, atoms: [37, 28, 37, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 11, 11, 11, 11, 11, 1, 37, 37, 37, 37, 37, 37, 28, 28, 1, 1, 6, 6, 11, 1, 1] 156 rigid atoms, others: [32, 4, 37, 6, 7, 8, 9, 10, 11, 12, 13, 22, 36, 31] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042455 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042455 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 1: /scratch/stefan/7921153/working/building/REAL250005042455/1.* 0: /scratch/stefan/7921153/working/building/REAL250005042455/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042455 Building REAL250005042456 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042456' /scratch/stefan/7921153/working/building/REAL250005042456 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042456 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042456/0 /scratch/stefan/7921153/working/building/REAL250005042456 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 565) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/565 `/scratch/stefan/7921153/working/3D/565' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CCC(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042456.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042456/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042456 none N#CCC(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [37, 37, 20, 13, 20, 13, 13, 13, 13, 13, 7, 13, 7, 1, 7, 1, 1, 1, 1, 1, 1, 13, 37, 37, 13, 13, 39, 7, 1, 13, 13] 111 rigid atoms, others: [13, 15, 16, 17, 18, 19, 20, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 29, 30]) total number of confs: 175 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042456 none N#CCC(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [15, 15, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 13, 13, 13, 13, 13, 1, 15, 15, 1, 1, 6, 7, 13, 1, 1] 111 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 11, 12, 21, 24, 25, 29, 30] set([0, 1, 2, 4, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 26, 27, 28]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042456 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042456 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042456/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042456 Building REAL250005042457 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042457' /scratch/stefan/7921153/working/building/REAL250005042457 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042457 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042457/0 /scratch/stefan/7921153/working/building/REAL250005042457 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 566) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/566 `/scratch/stefan/7921153/working/3D/566' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CN(C(=O)C2CC2F)C[C@H]1O)C1=CC(=O)[N-]O1) `REAL250005042457.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042457.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042457/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042457 none O=C(N[C@@H]1CN(C(=O)C2CC2F)C[C@H]1O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 15, 5, 5, 7, 12, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [5, 1, 5, 5, 9, 9, 9, 9, 12, 12, 25, 25, 25, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 5, 9, 9, 25, 25, 25, 25, 9, 9, 27, 1] 75 rigid atoms, others: [1, 33, 17, 18, 19, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 102 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: REAL250005042457 none O=C(N[C@@H]1CN(C(=O)C2CC2F)C[C@H]1O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 15, 5, 5, 7, 12, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [23, 23, 10, 10, 10, 10, 6, 1, 6, 1, 1, 1, 1, 10, 10, 10, 10, 23, 25, 25, 25, 25, 25, 23, 10, 10, 1, 1, 1, 1, 10, 10, 30, 25] 75 rigid atoms, others: [7, 9, 10, 11, 12, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33]) total number of confs: 97 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042457 none O=C(N[C@@H]1CN(C(=O)C2CC2F)C[C@H]1O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 15, 5, 5, 7, 12, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [6, 6, 1, 1, 1, 1, 1, 1, 3, 3, 10, 10, 10, 1, 1, 1, 1, 6, 9, 9, 9, 9, 9, 6, 1, 1, 10, 10, 10, 10, 1, 1, 3, 9] 75 rigid atoms, others: [2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 24, 25, 30, 31] set([0, 1, 33, 32, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042457 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042457 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042457/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042457 Building REAL250005042458 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042458' /scratch/stefan/7921153/working/building/REAL250005042458 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042458 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042458/0 /scratch/stefan/7921153/working/building/REAL250005042458 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 567) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/567 `/scratch/stefan/7921153/working/3D/567' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCF)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042458.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042458.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042458/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042458 none O=C(CCF)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'F', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 15, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 132 conformations in input total number of sets (complete confs): 132 using faster count positions algorithm for large data unique positions, atoms: [20, 12, 20, 44, 44, 12, 12, 12, 12, 12, 5, 12, 5, 1, 5, 1, 1, 1, 1, 1, 1, 12, 44, 44, 44, 44, 12, 12, 36, 5, 1, 12, 12] 132 rigid atoms, others: [13, 15, 16, 17, 18, 19, 20, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32]) total number of confs: 200 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042458 none O=C(CCF)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'F', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 15, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 132 conformations in input total number of sets (complete confs): 132 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 14, 20, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 12, 12, 1, 14, 14, 20, 20, 1, 1, 6, 6, 12, 1, 1] 132 rigid atoms, others: [32, 1, 5, 6, 7, 8, 9, 10, 11, 12, 21, 26, 27, 31] set([0, 2, 3, 4, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 28, 29, 30]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042458 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042458 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042458/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042458 Building REAL250005042459 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042459' /scratch/stefan/7921153/working/building/REAL250005042459 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042459 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042459/0 /scratch/stefan/7921153/working/building/REAL250005042459 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 568) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/568 `/scratch/stefan/7921153/working/3D/568' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H](C)C(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042459.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042459/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042459 none CO[C@H](C)C(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [31, 31, 22, 31, 31, 12, 22, 12, 12, 12, 12, 12, 6, 12, 6, 1, 6, 1, 1, 1, 1, 1, 1, 12, 31, 31, 31, 31, 31, 31, 12, 12, 36, 6, 1, 12, 12] 93 rigid atoms, others: [34, 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, 35, 36]) total number of confs: 144 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042459 none CO[C@H](C)C(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [18, 14, 7, 14, 14, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 12, 12, 12, 12, 12, 1, 18, 18, 18, 14, 14, 14, 1, 1, 6, 7, 12, 1, 1] 93 rigid atoms, others: [35, 36, 5, 7, 8, 9, 10, 11, 12, 13, 14, 23, 30, 31] set([0, 1, 2, 3, 4, 6, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 32, 33, 34]) total number of confs: 83 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042459 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042459 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042459/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042459 Building REAL250005042460 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042460' /scratch/stefan/7921153/working/building/REAL250005042460 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042460 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042460/0 /scratch/stefan/7921153/working/building/REAL250005042460 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 569) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/569 `/scratch/stefan/7921153/working/3D/569' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](O)C(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042460.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042460.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042460/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:2-3 Rotatable hydrogens reported. Reducing confs by a factor of 3 WARNING:root:Setting energy window to 12 and max confs to 66 ('energy: ', 12.0) ('conf: ', 66) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042460 none C[C@@H](O)C(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 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: [21, 13, 21, 21, 9, 13, 9, 9, 9, 9, 9, 7, 9, 7, 1, 7, 1, 1, 1, 1, 1, 1, 9, 21, 21, 21, 63, 9, 9, 27, 7, 1, 9, 9] 189 rigid atoms, others: [14, 16, 17, 18, 19, 20, 21, 31] 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, 32, 33]) total number of confs: 164 number of broken/clashed sets: 33 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042460 none C[C@@H](O)C(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 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: [9, 4, 9, 9, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 9, 9, 9, 9, 9, 1, 9, 9, 9, 27, 1, 1, 6, 5, 9, 1, 1] 189 rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 11, 12, 13, 22, 27, 28] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 29, 30, 31]) total number of confs: 78 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042460 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042460 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042460/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042460 Building REAL250005042461 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042461' /scratch/stefan/7921153/working/building/REAL250005042461 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042461 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042461/0 /scratch/stefan/7921153/working/building/REAL250005042461 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 570) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/570 `/scratch/stefan/7921153/working/3D/570' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C1CC1C(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042461.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042461.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042461/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042461 none C=C1CC1C(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 27, 13, 9, 13, 9, 9, 9, 9, 9, 6, 9, 6, 1, 6, 1, 1, 1, 1, 1, 1, 9, 27, 27, 27, 27, 27, 9, 9, 27, 6, 1, 9, 9] 81 rigid atoms, others: [32, 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, 33, 34]) total number of confs: 108 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: REAL250005042461 none C=C1CC1C(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 12, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 9, 9, 9, 9, 9, 1, 12, 12, 12, 12, 12, 1, 1, 6, 6, 9, 1, 1] 81 rigid atoms, others: [33, 34, 4, 6, 7, 8, 9, 10, 11, 12, 13, 22, 28, 29] set([0, 1, 2, 3, 5, 32, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 30, 31]) total number of confs: 51 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042461 none C=C1CC1C(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 7, 7, 12, 12, 12, 12, 12, 12, 12, 25, 25, 25, 27, 27, 27, 27, 27, 12, 1, 1, 1, 1, 1, 12, 12, 36, 25, 27, 12, 12] 81 rigid atoms, others: [0, 1, 2, 3, 4, 23, 24, 25, 26, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042461 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042461 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042461/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042461 Building REAL250005042462 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042462' /scratch/stefan/7921153/working/building/REAL250005042462 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042462 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042462/0 /scratch/stefan/7921153/working/building/REAL250005042462 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 571) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/571 `/scratch/stefan/7921153/working/3D/571' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC1C(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042462.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042462.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042462/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042462 none CC1=CC1C(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [34, 34, 34, 20, 12, 20, 12, 12, 12, 12, 12, 5, 12, 5, 1, 5, 1, 1, 1, 1, 1, 1, 12, 34, 34, 34, 34, 34, 12, 12, 36, 6, 1, 12, 12] 102 rigid atoms, others: [32, 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, 33, 34]) total number of confs: 141 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: REAL250005042462 none CC1=CC1C(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [18, 18, 18, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 12, 12, 1, 18, 18, 18, 18, 18, 1, 1, 6, 6, 12, 1, 1] 102 rigid atoms, others: [33, 34, 4, 6, 7, 8, 9, 10, 11, 12, 13, 22, 28, 29] set([0, 1, 2, 3, 5, 32, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 30, 31]) total number of confs: 72 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042462 none CC1=CC1C(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 102 conformations in input total number of sets (complete confs): 102 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 8, 8, 18, 18, 18, 18, 18, 18, 18, 32, 32, 32, 34, 34, 34, 34, 34, 18, 2, 2, 2, 1, 1, 18, 18, 54, 32, 34, 18, 18] 102 rigid atoms, others: [0, 1, 2, 3, 4, 26, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042462 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042462 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042462/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042462 Building REAL250005042463 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042463' /scratch/stefan/7921153/working/building/REAL250005042463 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042463 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042463/0 /scratch/stefan/7921153/working/building/REAL250005042463 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 572) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/572 `/scratch/stefan/7921153/working/3D/572' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042463.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042463.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042463/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042463 none C=CC(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [20, 20, 13, 20, 13, 13, 13, 13, 13, 8, 13, 8, 1, 8, 1, 1, 1, 1, 1, 1, 13, 20, 20, 20, 13, 13, 39, 8, 1, 13, 13] 60 rigid atoms, others: [12, 14, 15, 16, 17, 18, 19, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30]) total number of confs: 94 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042463 none C=CC(=O)N1C[C@@H](O)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [13, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 13, 13, 13, 13, 13, 1, 13, 13, 13, 1, 1, 6, 6, 13, 1, 1] 60 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 11, 20, 24, 25, 29, 30] set([0, 1, 3, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 26, 27, 28]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042463 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042463 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042463/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042463 Building REAL250005042464 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042464' /scratch/stefan/7921153/working/building/REAL250005042464 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042464 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042464/0 /scratch/stefan/7921153/working/building/REAL250005042464 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 573) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/573 `/scratch/stefan/7921153/working/3D/573' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N1CCCOC(CNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042464.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042464.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042464/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042464 none CCC(=O)N1CCCOC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 70, 108, 70, 70, 70, 70, 70, 31, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 70, 108, 108, 108, 108, 108, 70, 70, 70, 70, 70, 70, 70, 31, 31, 8, 1, 70, 70] 108 rigid atoms, others: [36, 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, 37, 38]) total number of confs: 331 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042464 none CCC(=O)N1CCCOC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [16, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 10, 49, 49, 49, 70, 70, 70, 70, 70, 1, 17, 17, 17, 16, 16, 1, 1, 1, 1, 1, 1, 1, 10, 10, 49, 70, 1, 1] 108 rigid atoms, others: [32, 2, 4, 5, 6, 7, 8, 9, 10, 38, 37, 20, 26, 27, 28, 29, 30, 31] set([0, 1, 34, 3, 36, 35, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25]) total number of confs: 226 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042464 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042464 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042464/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042464 Building REAL250005042465 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042465' /scratch/stefan/7921153/working/building/REAL250005042465 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042465 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042465/0 /scratch/stefan/7921153/working/building/REAL250005042465 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 574) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/574 `/scratch/stefan/7921153/working/3D/574' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCCOC(CNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042465.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042465/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042465 none CC(=O)N1CCCOC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [47, 36, 47, 36, 36, 36, 36, 36, 18, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 36, 47, 47, 47, 36, 36, 36, 36, 36, 36, 36, 17, 17, 8, 1, 36, 36] 47 rigid atoms, others: [33, 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, 34, 35]) total number of confs: 157 number of broken/clashed sets: 26 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042465 none CC(=O)N1CCCOC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 10, 32, 32, 32, 36, 36, 36, 36, 36, 1, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 10, 10, 32, 36, 1, 1] 47 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 8, 9, 19, 23, 24, 25, 26, 27, 28, 29, 35] set([0, 32, 2, 33, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 30, 31]) total number of confs: 110 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042465 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042465 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042465/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042465 Building REAL250005042466 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042466' /scratch/stefan/7921153/working/building/REAL250005042466 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042466 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042466/0 /scratch/stefan/7921153/working/building/REAL250005042466 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 575) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/575 `/scratch/stefan/7921153/working/3D/575' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CO)N1CCCOC(CNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042466.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042466.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042466/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042466 none O=C(CO)N1CCCOC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 5, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 195 conformations in input total number of sets (complete confs): 195 using faster count positions algorithm for large data unique positions, atoms: [57, 48, 57, 65, 48, 48, 48, 48, 48, 23, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 48, 65, 65, 195, 48, 48, 48, 48, 48, 48, 48, 23, 23, 8, 1, 48, 48] 195 rigid atoms, others: [34, 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, 35, 36]) total number of confs: 423 number of broken/clashed sets: 32 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042466 none O=C(CO)N1CCCOC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 5, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 195 conformations in input total number of sets (complete confs): 195 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 19, 1, 1, 1, 1, 1, 1, 1, 10, 37, 37, 37, 48, 48, 48, 48, 48, 1, 19, 19, 57, 1, 1, 1, 1, 1, 1, 1, 10, 10, 37, 48, 1, 1] 195 rigid atoms, others: [1, 35, 4, 5, 6, 7, 8, 9, 10, 20, 24, 25, 26, 27, 28, 29, 30, 36] set([0, 32, 2, 3, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 34, 31]) total number of confs: 246 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042466 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042466 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042466/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042466 Building REAL250005042467 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042467' /scratch/stefan/7921153/working/building/REAL250005042467 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042467 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042467/0 /scratch/stefan/7921153/working/building/REAL250005042467 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 576) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/576 `/scratch/stefan/7921153/working/3D/576' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)NCC1CN(C(=O)C2=CC(=O)[N-]O2)CCCO1) `REAL250005042467.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042467.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042467/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042467 none CCC(=O)NCC1CN(C(=O)C2=CC(=O)[N-]O2)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 12, 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, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 41, 41, 41, 30, 11, 11, 11, 6, 1, 6, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 59, 59, 59, 59, 59, 41, 30, 30, 11, 11, 11, 1, 11, 11, 11, 11, 11, 11] 59 rigid atoms, others: [32, 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, 33, 34, 35, 36, 37, 38]) total number of confs: 248 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042467 none CCC(=O)NCC1CN(C(=O)C2=CC(=O)[N-]O2)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 12, 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, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [40, 22, 22, 22, 7, 1, 1, 1, 1, 1, 6, 6, 11, 11, 11, 11, 11, 1, 1, 1, 1, 40, 40, 40, 40, 40, 22, 7, 7, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1] 59 rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 38, 17, 18, 19, 20, 37, 29, 30, 31] set([0, 1, 2, 3, 4, 32, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042467 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042467 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042467/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042467 Building REAL250005042468 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042468' /scratch/stefan/7921153/working/building/REAL250005042468 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042468 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042468/0 /scratch/stefan/7921153/working/building/REAL250005042468 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 577) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/577 `/scratch/stefan/7921153/working/3D/577' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC1CN(C(=O)C2=CC(=O)[N-]O2)CCCO1) `REAL250005042468.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042468.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042468/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042468 none CC(=O)NCC1CN(C(=O)C2=CC(=O)[N-]O2)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 33, 14, 14, 14, 7, 1, 7, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 36, 36, 36, 36, 33, 33, 14, 14, 14, 1, 14, 14, 14, 14, 14, 14] 36 rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35]) total number of confs: 119 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042468 none CC(=O)NCC1CN(C(=O)C2=CC(=O)[N-]O2)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [18, 18, 18, 7, 1, 1, 1, 1, 1, 7, 7, 14, 14, 14, 14, 14, 1, 1, 1, 1, 19, 19, 19, 18, 7, 7, 1, 1, 1, 14, 1, 1, 1, 1, 1, 1] 36 rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 16, 17, 18, 19, 26, 27, 28, 30, 31] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 29]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042468 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042468 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042468/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042468 Building REAL250005042469 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042469' /scratch/stefan/7921153/working/building/REAL250005042469 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042469 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042469/0 /scratch/stefan/7921153/working/building/REAL250005042469 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 578) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/578 `/scratch/stefan/7921153/working/3D/578' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CO)NCC1CN(C(=O)C2=CC(=O)[N-]O2)CCCO1) `REAL250005042469.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042469/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042469 none O=C(CO)NCC1CN(C(=O)C2=CC(=O)[N-]O2)CCCO1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 12, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 408 conformations in input total number of sets (complete confs): 408 using faster count positions algorithm for large data unique positions, atoms: [135, 135, 135, 136, 90, 28, 28, 28, 11, 1, 11, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 136, 136, 408, 135, 90, 90, 28, 28, 28, 1, 28, 28, 28, 28, 28, 28] 408 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36]) total number of confs: 873 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042469 none O=C(CO)NCC1CN(C(=O)C2=CC(=O)[N-]O2)CCCO1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 12, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 408 conformations in input total number of sets (complete confs): 408 using faster count positions algorithm for large data unique positions, atoms: [45, 45, 45, 86, 9, 1, 1, 1, 1, 1, 7, 7, 28, 28, 28, 28, 28, 1, 1, 1, 1, 86, 86, 258, 45, 9, 9, 1, 1, 1, 28, 1, 1, 1, 1, 1, 1] 408 rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 17, 18, 19, 20, 27, 28, 29, 31] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 30]) total number of confs: 610 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042469 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042469 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042469/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042469 Building REAL250005042470 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042470' /scratch/stefan/7921153/working/building/REAL250005042470 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042470 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042470/0 /scratch/stefan/7921153/working/building/REAL250005042470 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 579) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/579 `/scratch/stefan/7921153/working/3D/579' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(=O)NCC1CN(C(=O)C2=CC(=O)[N-]O2)CCCO1) `REAL250005042470.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042470/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042470 none C=CC(=O)NCC1CN(C(=O)C2=CC(=O)[N-]O2)CCCO1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 24, 10, 10, 10, 6, 1, 6, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 33, 33, 33, 33, 24, 24, 10, 10, 10, 1, 10, 10, 10, 10, 10, 10] 33 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36]) total number of confs: 113 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042470 none C=CC(=O)NCC1CN(C(=O)C2=CC(=O)[N-]O2)CCCO1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [23, 20, 20, 20, 8, 1, 1, 1, 1, 1, 5, 5, 10, 10, 10, 10, 10, 1, 1, 1, 1, 23, 23, 23, 20, 8, 8, 1, 1, 1, 10, 1, 1, 1, 1, 1, 1] 33 rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 17, 18, 19, 20, 27, 28, 29, 31] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 30]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042470 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042470 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042470/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042470 Building REAL250005042471 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042471' /scratch/stefan/7921153/working/building/REAL250005042471 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042471 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042471/0 /scratch/stefan/7921153/working/building/REAL250005042471 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 580) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/580 `/scratch/stefan/7921153/working/3D/580' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)NC1CC(NC(=O)C2=CC(=O)[N-]O2)C12CCC2) `REAL250005042471.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042471.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042471/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042471 none CCC(=O)NC1CC(NC(=O)C2=CC(=O)[N-]O2)C12CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 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, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [34, 24, 24, 24, 16, 16, 16, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 34, 34, 34, 34, 34, 24, 16, 16, 16, 16, 6, 1, 16, 16, 16, 16, 16, 16] 34 rigid atoms, others: [32, 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, 33, 34, 35, 36, 37, 38]) total number of confs: 137 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042471 none CCC(=O)NC1CC(NC(=O)C2=CC(=O)[N-]O2)C12CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 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, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [19, 5, 5, 5, 1, 1, 1, 1, 1, 6, 6, 6, 16, 16, 16, 16, 16, 1, 1, 1, 1, 19, 19, 19, 19, 19, 5, 1, 1, 1, 1, 6, 16, 1, 1, 1, 1, 1, 1] 34 rigid atoms, others: [33, 34, 35, 4, 5, 6, 7, 8, 38, 17, 18, 19, 20, 36, 27, 28, 29, 30, 37] set([0, 1, 2, 3, 32, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 31]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042471 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042471 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042471/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042471 Building REAL250005042472 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042472' /scratch/stefan/7921153/working/building/REAL250005042472 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042472 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042472/0 /scratch/stefan/7921153/working/building/REAL250005042472 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 581) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/581 `/scratch/stefan/7921153/working/3D/581' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC1CC(NC(=O)C2=CC(=O)[N-]O2)C12CCC2) `REAL250005042472.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042472.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042472/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042472 none CC(=O)NC1CC(NC(=O)C2=CC(=O)[N-]O2)C12CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 12, 12, 12, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 1, 12, 12, 12, 12, 12, 12] 12 rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35]) total number of confs: 29 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042472 none CC(=O)NC1CC(NC(=O)C2=CC(=O)[N-]O2)C12CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 5, 5, 1, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 12, 12, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 1, 6, 12, 1, 1, 1, 1, 1, 1] 12 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 16, 17, 18, 19, 24, 25, 26, 27, 35, 30, 31] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 28, 29]) total number of confs: 32 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042472 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042472 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042472/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042472 Building REAL250005042473 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042473' /scratch/stefan/7921153/working/building/REAL250005042473 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042473 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042473/0 /scratch/stefan/7921153/working/building/REAL250005042473 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 582) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/582 `/scratch/stefan/7921153/working/3D/582' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CO)NC1CC(NC(=O)C2=CC(=O)[N-]O2)C12CCC2) `REAL250005042473.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042473/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042473 none O=C(CO)NC1CC(NC(=O)C2=CC(=O)[N-]O2)C12CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 18, 21, 12, 12, 12, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 21, 21, 63, 18, 12, 12, 12, 12, 6, 1, 12, 12, 12, 12, 12, 12] 63 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36]) total number of confs: 136 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042473 none O=C(CO)NC1CC(NC(=O)C2=CC(=O)[N-]O2)C12CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 17, 1, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 12, 12, 1, 1, 1, 1, 17, 17, 51, 5, 1, 1, 1, 1, 6, 12, 1, 1, 1, 1, 1, 1] 63 rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 36, 17, 18, 19, 20, 25, 26, 27, 28, 31] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 29, 30]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042473 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042473 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042473/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042473 Building REAL250005042474 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042474' /scratch/stefan/7921153/working/building/REAL250005042474 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042474 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042474/0 /scratch/stefan/7921153/working/building/REAL250005042474 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 583) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/583 `/scratch/stefan/7921153/working/3D/583' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)NC1CC(NC(=O)C2=CC(=O)[N-]O2)C12CCC2) `REAL250005042474.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042474/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042474 none CCC(=O)NC1CC(NC(=O)C2=CC(=O)[N-]O2)C12CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 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, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [34, 24, 24, 24, 16, 16, 16, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 34, 34, 34, 34, 34, 24, 16, 16, 16, 16, 6, 1, 16, 16, 16, 16, 16, 16] 34 rigid atoms, others: [32, 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, 33, 34, 35, 36, 37, 38]) total number of confs: 137 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042474 none CCC(=O)NC1CC(NC(=O)C2=CC(=O)[N-]O2)C12CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 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, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [19, 5, 5, 5, 1, 1, 1, 1, 1, 6, 6, 6, 16, 16, 16, 16, 16, 1, 1, 1, 1, 19, 19, 19, 19, 19, 5, 1, 1, 1, 1, 6, 16, 1, 1, 1, 1, 1, 1] 34 rigid atoms, others: [33, 34, 35, 4, 5, 6, 7, 8, 38, 17, 18, 19, 20, 36, 27, 28, 29, 30, 37] set([0, 1, 2, 3, 32, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 31]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042474 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042474 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042474/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042474 Building REAL250005042475 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042475' /scratch/stefan/7921153/working/building/REAL250005042475 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042475 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042475/0 /scratch/stefan/7921153/working/building/REAL250005042475 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 584) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/584 `/scratch/stefan/7921153/working/3D/584' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC1CC(NC(=O)C2=CC(=O)[N-]O2)C12CCC2) `REAL250005042475.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042475.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042475/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042475 none CC(=O)NC1CC(NC(=O)C2=CC(=O)[N-]O2)C12CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 12, 12, 12, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 1, 12, 12, 12, 12, 12, 12] 12 rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35]) total number of confs: 29 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042475 none CC(=O)NC1CC(NC(=O)C2=CC(=O)[N-]O2)C12CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 5, 5, 1, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 12, 12, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 1, 6, 12, 1, 1, 1, 1, 1, 1] 12 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 16, 17, 18, 19, 24, 25, 26, 27, 35, 30, 31] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 28, 29]) total number of confs: 32 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042475 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042475 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042475/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042475 Building REAL250005042476 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042476' /scratch/stefan/7921153/working/building/REAL250005042476 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042476 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042476/0 /scratch/stefan/7921153/working/building/REAL250005042476 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 585) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/585 `/scratch/stefan/7921153/working/3D/585' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CO)NC1CC(NC(=O)C2=CC(=O)[N-]O2)C12CCC2) `REAL250005042476.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042476.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042476/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042476 none O=C(CO)NC1CC(NC(=O)C2=CC(=O)[N-]O2)C12CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 18, 21, 12, 12, 12, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 21, 21, 63, 18, 12, 12, 12, 12, 6, 1, 12, 12, 12, 12, 12, 12] 63 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36]) total number of confs: 136 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042476 none O=C(CO)NC1CC(NC(=O)C2=CC(=O)[N-]O2)C12CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 17, 1, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 12, 12, 1, 1, 1, 1, 17, 17, 51, 5, 1, 1, 1, 1, 6, 12, 1, 1, 1, 1, 1, 1] 63 rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 36, 17, 18, 19, 20, 25, 26, 27, 28, 31] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 29, 30]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042476 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042476 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042476/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042476 Building REAL250005042477 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042477' /scratch/stefan/7921153/working/building/REAL250005042477 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042477 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042477/0 /scratch/stefan/7921153/working/building/REAL250005042477 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 586) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/586 `/scratch/stefan/7921153/working/3D/586' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(=O)NC1CC(NC(=O)C2=CC(=O)[N-]O2)C12CCC2) `REAL250005042477.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042477.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042477/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042477 none C=CC(=O)NC1CC(NC(=O)C2=CC(=O)[N-]O2)C12CCC2 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 24, 16, 16, 16, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 24, 24, 24, 24, 16, 16, 16, 16, 6, 1, 16, 16, 16, 16, 16, 16] 24 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36]) total number of confs: 69 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042477 none C=CC(=O)NC1CC(NC(=O)C2=CC(=O)[N-]O2)C12CCC2 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [14, 5, 5, 5, 1, 1, 1, 1, 1, 6, 6, 6, 16, 16, 16, 16, 16, 1, 1, 1, 1, 14, 14, 14, 5, 1, 1, 1, 1, 6, 16, 1, 1, 1, 1, 1, 1] 24 rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 36, 17, 18, 19, 20, 25, 26, 27, 28, 31] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 29, 30]) total number of confs: 63 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042477 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042477 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042477/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042477 Building REAL250005042478 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042478' /scratch/stefan/7921153/working/building/REAL250005042478 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042478 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042478/0 /scratch/stefan/7921153/working/building/REAL250005042478 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 587) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/587 `/scratch/stefan/7921153/working/3D/587' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N1CC2CCC1C(NC(=O)C1=CC(=O)[N-]O1)C2) `REAL250005042478.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042478/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042478 none CCC(=O)N1CC2CCC1C(NC(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 12, 21, 12, 12, 12, 12, 12, 12, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 12, 21, 21, 21, 21, 21, 12, 12, 12, 12, 12, 12, 12, 12, 12, 7, 1, 12, 12] 21 rigid atoms, others: [36, 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, 37, 38]) total number of confs: 61 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042478 none CCC(=O)N1CC2CCC1C(NC(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 12, 12, 1, 10, 10, 10, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 12, 1, 1] 21 rigid atoms, others: [32, 33, 2, 4, 5, 6, 7, 8, 9, 10, 11, 34, 38, 37, 20, 26, 27, 28, 29, 30, 31] set([0, 1, 3, 36, 35, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25]) total number of confs: 56 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042478 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042478 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042478/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042478 Building REAL250005042479 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042479' /scratch/stefan/7921153/working/building/REAL250005042479 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042479 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042479/0 /scratch/stefan/7921153/working/building/REAL250005042479 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 588) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/588 `/scratch/stefan/7921153/working/3D/588' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CC2CCC1C(NC(=O)C1=CC(=O)[N-]O1)C2) `REAL250005042479.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042479/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042479 none CC(=O)N1CC2CCC1C(NC(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 9, 13, 9, 9, 9, 9, 9, 9, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 9, 13, 13, 13, 9, 9, 9, 9, 9, 9, 9, 9, 9, 7, 1, 9, 9] 13 rigid atoms, others: [33, 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, 34, 35]) total number of confs: 37 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042479 none CC(=O)N1CC2CCC1C(NC(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 9, 9, 9, 9, 9, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 1, 1] 13 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 8, 9, 10, 35, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 32, 2, 33, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22]) total number of confs: 32 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042479 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042479 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042479/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042479 Building REAL250005042480 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042480' /scratch/stefan/7921153/working/building/REAL250005042480 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042480 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042480/0 /scratch/stefan/7921153/working/building/REAL250005042480 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 589) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/589 `/scratch/stefan/7921153/working/3D/589' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CO)N1CC2CCC1C(NC(=O)C1=CC(=O)[N-]O1)C2) `REAL250005042480.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042480.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042480/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042480 none O=C(CO)N1CC2CCC1C(NC(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [22, 13, 22, 22, 13, 13, 13, 13, 13, 13, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 13, 22, 22, 66, 13, 13, 13, 13, 13, 13, 13, 13, 13, 7, 1, 13, 13] 66 rigid atoms, others: [34, 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, 35, 36]) total number of confs: 129 number of broken/clashed sets: 14 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042480 none O=C(CO)N1CC2CCC1C(NC(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 13, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 13, 13, 13, 13, 13, 1, 13, 13, 39, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 13, 1, 1] 66 rigid atoms, others: [32, 1, 35, 4, 5, 6, 7, 8, 9, 10, 11, 36, 20, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 33, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 34]) total number of confs: 109 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042480 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042480 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042480/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042480 Building REAL250005042481 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042481' /scratch/stefan/7921153/working/building/REAL250005042481 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042481 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042481/0 /scratch/stefan/7921153/working/building/REAL250005042481 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 590) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/590 `/scratch/stefan/7921153/working/3D/590' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)NC1CC2CCC1N(C(=O)C1=CC(=O)[N-]O1)C2) `REAL250005042481.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042481/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042481 none CCC(=O)NC1CC2CCC1N(C(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 51, 51, 51, 27, 27, 27, 27, 27, 27, 27, 9, 1, 9, 1, 1, 1, 1, 1, 1, 27, 62, 62, 62, 62, 62, 51, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 27, 27] 62 rigid atoms, others: [36, 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, 37, 38]) total number of confs: 195 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042481 none CCC(=O)NC1CC2CCC1N(C(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [29, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 27, 27, 27, 27, 27, 1, 29, 29, 29, 29, 29, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 1, 1] 62 rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 11, 12, 38, 37, 20, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 36, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042481 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042481 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042481/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042481 Building REAL250005042482 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042482' /scratch/stefan/7921153/working/building/REAL250005042482 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042482 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042482/0 /scratch/stefan/7921153/working/building/REAL250005042482 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 591) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/591 `/scratch/stefan/7921153/working/3D/591' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC1CC2CCC1N(C(=O)C1=CC(=O)[N-]O1)C2) `REAL250005042482.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042482.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042482/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042482 none CC(=O)NC1CC2CCC1N(C(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 17, 17, 17, 17, 17, 17, 17, 7, 1, 7, 1, 1, 1, 1, 1, 1, 17, 20, 20, 20, 20, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 17, 17] 20 rigid atoms, others: [33, 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, 34, 35]) total number of confs: 42 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042482 none CC(=O)NC1CC2CCC1N(C(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 17, 17, 17, 17, 17, 1, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1] 20 rigid atoms, others: [32, 35, 34, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 33, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23]) total number of confs: 40 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042482 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042482 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042482/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042482 Building REAL250005042483 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042483' /scratch/stefan/7921153/working/building/REAL250005042483 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042483 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042483/0 /scratch/stefan/7921153/working/building/REAL250005042483 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 592) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/592 `/scratch/stefan/7921153/working/3D/592' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CO)NC1CC2CCC1N(C(=O)C1=CC(=O)[N-]O1)C2) `REAL250005042483.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042483.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042483/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042483 none O=C(CO)NC1CC2CCC1N(C(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [35, 35, 35, 42, 22, 22, 22, 22, 22, 22, 21, 9, 1, 9, 1, 1, 1, 1, 1, 1, 22, 42, 42, 126, 35, 22, 22, 22, 22, 22, 22, 22, 22, 21, 1, 22, 22] 126 rigid atoms, others: [34, 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, 35, 36]) total number of confs: 254 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042483 none O=C(CO)NC1CC2CCC1N(C(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [6, 6, 6, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 21, 21, 21, 21, 21, 1, 25, 25, 75, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 1, 1] 126 rigid atoms, others: [32, 33, 35, 4, 5, 6, 7, 8, 9, 10, 11, 12, 36, 20, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 34, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042483 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042483 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042483/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042483 Building REAL250005042484 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042484' /scratch/stefan/7921153/working/building/REAL250005042484 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042484 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042484/0 /scratch/stefan/7921153/working/building/REAL250005042484 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 593) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/593 `/scratch/stefan/7921153/working/3D/593' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(=O)NC1CC2CCC1N(C(=O)C1=CC(=O)[N-]O1)C2) `REAL250005042484.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042484.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042484/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042484 none C=CC(=O)NC1CC2CCC1N(C(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 37, 27, 27, 27, 27, 27, 27, 26, 9, 1, 9, 1, 1, 1, 1, 1, 1, 27, 37, 37, 37, 37, 27, 27, 27, 27, 27, 27, 27, 27, 26, 1, 27, 27] 37 rigid atoms, others: [34, 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, 35, 36]) total number of confs: 85 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042484 none C=CC(=O)NC1CC2CCC1N(C(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [11, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 26, 26, 26, 26, 26, 1, 11, 11, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 1, 1] 37 rigid atoms, others: [32, 33, 35, 4, 5, 6, 7, 8, 9, 10, 11, 12, 36, 20, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 34, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042484 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042484 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042484/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042484 Building REAL250005042485 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042485' /scratch/stefan/7921153/working/building/REAL250005042485 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042485 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042485/0 /scratch/stefan/7921153/working/building/REAL250005042485 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 594) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/594 `/scratch/stefan/7921153/working/3D/594' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005042485.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042485.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042485/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042485 none CCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [59, 46, 46, 46, 26, 26, 26, 26, 10, 1, 10, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 59, 59, 59, 59, 59, 46, 26, 26, 1, 26, 26, 26, 26, 26] 59 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34]) total number of confs: 191 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042485 none CCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [39, 6, 6, 6, 1, 1, 1, 1, 1, 1, 5, 5, 26, 26, 26, 26, 26, 1, 1, 1, 1, 39, 39, 39, 39, 39, 6, 1, 1, 26, 1, 1, 2, 2, 2] 59 rigid atoms, others: [4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 27, 28, 30, 31] set([0, 1, 2, 3, 33, 32, 10, 11, 12, 13, 14, 15, 16, 34, 21, 22, 23, 24, 25, 26, 29]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042485 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042485 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042485/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042485 Building REAL250005042486 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042486' /scratch/stefan/7921153/working/building/REAL250005042486 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042486 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042486/0 /scratch/stefan/7921153/working/building/REAL250005042486 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 595) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/595 `/scratch/stefan/7921153/working/3D/595' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005042486.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042486.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042486/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042486 none COCCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 173, 83, 83, 83, 30, 30, 30, 30, 10, 1, 10, 1, 1, 1, 1, 1, 1, 29, 30, 30, 30, 191, 191, 191, 191, 191, 173, 173, 83, 30, 30, 1, 30, 30, 30, 30, 30] 191 rigid atoms, others: [33, 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, 34, 35, 36, 37, 38]) total number of confs: 723 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042486 none COCCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [111, 68, 37, 6, 6, 6, 1, 1, 1, 1, 1, 1, 7, 7, 30, 30, 30, 30, 30, 1, 1, 1, 1, 111, 111, 111, 68, 68, 37, 37, 6, 1, 1, 30, 1, 1, 2, 2, 2] 191 rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 33, 36, 37, 38]) total number of confs: 409 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042486 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042486 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042486/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042486 Building REAL250005042487 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042487' /scratch/stefan/7921153/working/building/REAL250005042487 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042487 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042487/0 /scratch/stefan/7921153/working/building/REAL250005042487 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 596) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/596 `/scratch/stefan/7921153/working/3D/596' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005042487.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042487.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042487/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042487 none CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 18, 18, 18, 18, 8, 1, 8, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 21, 21, 21, 21, 18, 18, 1, 18, 18, 18, 18, 18] 21 rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31]) total number of confs: 46 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042487 none CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 18, 18, 18, 18, 18, 1, 1, 1, 1, 6, 6, 6, 6, 1, 1, 18, 1, 1, 2, 2, 2] 21 rigid atoms, others: [3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 24, 25, 27, 28] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 26, 29, 30, 31]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042487 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042487 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042487/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042487 Building REAL250005042488 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042488' /scratch/stefan/7921153/working/building/REAL250005042488 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042488 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042488/0 /scratch/stefan/7921153/working/building/REAL250005042488 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 597) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/597 `/scratch/stefan/7921153/working/3D/597' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C1CC1) `REAL250005042488.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042488/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042488 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 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: [28, 28, 28, 28, 28, 28, 59, 59, 76, 76, 76, 76, 76, 28, 12, 28, 12, 1, 12, 1, 1, 1, 28, 28, 28, 28, 28, 76, 28, 28, 12, 1, 1, 1, 1, 1] 76 rigid atoms, others: [32, 33, 34, 35, 17, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 205 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: REAL250005042488 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 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: [26, 26, 26, 25, 9, 1, 9, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 47, 47, 47, 76, 76, 26, 26, 26, 25, 25, 1, 26, 26, 47, 76, 76, 76, 76, 76] 76 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 27] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 208 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042488 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 76 conformations in input total number of sets (complete confs): 76 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 25, 25, 25, 26, 26, 1, 1, 1, 1, 5, 5, 5, 28, 28, 2, 2, 2, 1, 1, 25, 1, 1, 5, 28, 28, 28, 28, 28] 76 rigid atoms, others: [0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 25, 26, 28, 29] set([6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 27, 30, 31, 32, 33, 34, 35]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042488 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042488 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042488/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042488 Building REAL250005042489 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042489' /scratch/stefan/7921153/working/building/REAL250005042489 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042489 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042489/0 /scratch/stefan/7921153/working/building/REAL250005042489 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 598) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/598 `/scratch/stefan/7921153/working/3D/598' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C1CCC1) `REAL250005042489.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042489.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042489/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042489 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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] 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: [32, 32, 32, 32, 32, 32, 65, 65, 77, 77, 77, 77, 77, 32, 12, 32, 12, 1, 12, 1, 1, 1, 1, 32, 32, 32, 32, 32, 77, 32, 32, 12, 1, 1, 1, 1, 1, 1, 1] 77 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 17, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 216 number of broken/clashed sets: 1 ./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: REAL250005042489 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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] 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: [20, 20, 20, 20, 9, 1, 9, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 41, 41, 41, 77, 77, 77, 20, 20, 20, 20, 20, 1, 20, 20, 41, 77, 77, 77, 77, 77, 77, 77] 77 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 213 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042489 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 20, 20, 20, 20, 20, 1, 1, 1, 1, 6, 6, 6, 32, 32, 32, 2, 2, 2, 1, 1, 20, 1, 1, 6, 32, 32, 32, 32, 32, 32, 32] 77 rigid atoms, others: [0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 26, 27, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 112 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042489 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042489 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042489/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042489 Building REAL250005042490 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042490' /scratch/stefan/7921153/working/building/REAL250005042490 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042490 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042490/0 /scratch/stefan/7921153/working/building/REAL250005042490 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 599) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/599 `/scratch/stefan/7921153/working/3D/599' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)CC1CC1) `REAL250005042490.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042490/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042490 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)CC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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] 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: [70, 70, 70, 70, 70, 70, 115, 115, 141, 141, 141, 141, 141, 70, 23, 70, 23, 3, 23, 1, 1, 1, 1, 70, 70, 70, 70, 70, 141, 70, 70, 23, 3, 3, 1, 1, 1, 1, 1] 141 rigid atoms, others: [34, 35, 36, 37, 38, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 391 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: REAL250005042490 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)CC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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] 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: [28, 28, 28, 28, 9, 1, 9, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 61, 61, 61, 118, 141, 141, 28, 28, 28, 28, 28, 1, 28, 28, 61, 118, 118, 141, 141, 141, 141, 141] 141 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 514 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042490 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)CC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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] 0 hydrogens need rotated 141 conformations in input total number of sets (complete confs): 141 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 7, 28, 28, 28, 28, 28, 1, 1, 1, 1, 6, 6, 6, 46, 70, 70, 2, 2, 2, 1, 1, 28, 1, 1, 6, 46, 46, 70, 70, 70, 70, 70] 141 rigid atoms, others: [0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 26, 27, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 290 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042490 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042490 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042490/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042490 Building REAL250005042491 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042491' /scratch/stefan/7921153/working/building/REAL250005042491 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042491 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042491/0 /scratch/stefan/7921153/working/building/REAL250005042491 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 600) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/600 `/scratch/stefan/7921153/working/3D/600' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C(C)(C)F) `REAL250005042491.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042491/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042491 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C(C)(C)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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] 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: [24, 24, 24, 24, 10, 1, 10, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 50, 50, 50, 67, 67, 67, 24, 24, 24, 24, 24, 1, 24, 24, 50, 67, 67, 67, 67, 67, 67] 67 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 211 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042491 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C(C)(C)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 5, 24, 24, 24, 24, 24, 1, 1, 1, 1, 6, 6, 6, 33, 33, 33, 2, 2, 2, 1, 1, 24, 1, 1, 6, 33, 33, 33, 33, 33, 33] 67 rigid atoms, others: [0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 26, 27, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042491 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042491 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042491/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042491 Building REAL250005042492 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042492' /scratch/stefan/7921153/working/building/REAL250005042492 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042492 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042492/0 /scratch/stefan/7921153/working/building/REAL250005042492 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 601) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/601 `/scratch/stefan/7921153/working/3D/601' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005042492.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042492/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042492 none COCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [94, 94, 61, 61, 61, 24, 24, 24, 24, 9, 1, 9, 1, 1, 1, 1, 1, 1, 23, 23, 24, 23, 94, 94, 94, 94, 94, 61, 24, 24, 1, 23, 23, 24, 24, 24] 94 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35]) total number of confs: 336 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042492 none COCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [48, 34, 6, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 23, 24, 24, 24, 24, 1, 1, 1, 1, 48, 48, 48, 34, 34, 6, 1, 1, 23, 1, 1, 2, 2, 2] 94 rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 28, 29, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 30, 33, 34, 35]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042492 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042492 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042492/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042492 Building REAL250005042493 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042493' /scratch/stefan/7921153/working/building/REAL250005042493 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042493 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042493/0 /scratch/stefan/7921153/working/building/REAL250005042493 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 602) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/602 `/scratch/stefan/7921153/working/3D/602' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005042493.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042493/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042493 none CCCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 135, 73, 73, 73, 32, 32, 32, 32, 10, 1, 10, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 136, 136, 136, 136, 136, 135, 135, 73, 32, 32, 1, 32, 32, 32, 32, 32] 136 rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37]) total number of confs: 478 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042493 none CCCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [57, 37, 6, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 32, 32, 32, 32, 32, 1, 1, 1, 1, 67, 67, 67, 67, 67, 37, 37, 6, 1, 1, 32, 1, 1, 2, 2, 2] 136 rigid atoms, others: [33, 34, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 32, 35, 36, 37]) total number of confs: 390 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042493 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042493 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042493/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042493 Building REAL250005042494 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042494' /scratch/stefan/7921153/working/building/REAL250005042494 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042494 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042494/0 /scratch/stefan/7921153/working/building/REAL250005042494 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 603) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/603 `/scratch/stefan/7921153/working/3D/603' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005042494.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042494/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042494 none CC(C)CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [90, 88, 90, 48, 48, 48, 24, 24, 24, 24, 9, 1, 9, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 90, 90, 90, 90, 90, 90, 90, 88, 88, 48, 24, 24, 1, 24, 24, 24, 24, 24] 90 rigid atoms, others: [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, 34, 36, 37, 38, 39, 40]) total number of confs: 309 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042494 none CC(C)CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [28, 26, 35, 6, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 24, 24, 24, 24, 24, 1, 1, 1, 1, 35, 35, 35, 35, 35, 35, 35, 26, 26, 6, 1, 1, 24, 1, 1, 2, 2, 2] 90 rigid atoms, others: [33, 34, 36, 37, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 38, 39, 40]) total number of confs: 226 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042494 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042494 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042494/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042494 Building REAL250005042495 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042495' /scratch/stefan/7921153/working/building/REAL250005042495 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042495 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042495/0 /scratch/stefan/7921153/working/building/REAL250005042495 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 604) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/604 `/scratch/stefan/7921153/working/3D/604' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005042495.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042495/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042495 none CC1CC1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 49, 49, 49, 23, 24, 24, 23, 7, 1, 7, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 74, 74, 74, 74, 74, 74, 74, 49, 23, 23, 1, 24, 24, 24, 24, 24] 74 rigid atoms, others: [33, 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, 34, 35, 36, 37, 38]) total number of confs: 218 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: REAL250005042495 none CC1CC1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [31, 31, 31, 6, 6, 6, 1, 1, 1, 1, 1, 1, 5, 6, 24, 24, 24, 24, 24, 1, 1, 1, 1, 31, 31, 31, 31, 31, 31, 31, 6, 1, 1, 24, 1, 1, 2, 2, 2] 74 rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 33, 36, 37, 38]) total number of confs: 113 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042495 none CC1CC1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 10, 10, 10, 31, 31, 31, 31, 67, 67, 74, 74, 74, 74, 74, 31, 31, 31, 31, 2, 2, 2, 1, 1, 1, 1, 10, 31, 31, 74, 31, 31, 31, 31, 31] 74 rigid atoms, others: [0, 1, 2, 3, 4, 26, 27, 28, 29] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042495 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042495 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042495/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042495 Building REAL250005042496 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042496' /scratch/stefan/7921153/working/building/REAL250005042496 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042496 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042496/0 /scratch/stefan/7921153/working/building/REAL250005042496 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 605) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/605 `/scratch/stefan/7921153/working/3D/605' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005042496.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042496.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042496/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042496 none CCOCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 156 conformations in input total number of sets (complete confs): 156 using faster count positions algorithm for large data unique positions, atoms: [156, 156, 149, 75, 75, 75, 28, 28, 28, 28, 10, 1, 10, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 156, 156, 156, 156, 156, 149, 149, 75, 28, 28, 1, 28, 28, 28, 28, 28] 156 rigid atoms, others: [33, 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, 34, 35, 36, 37, 38]) total number of confs: 525 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042496 none CCOCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 156 conformations in input total number of sets (complete confs): 156 using faster count positions algorithm for large data unique positions, atoms: [99, 90, 42, 6, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 28, 28, 28, 28, 28, 1, 1, 1, 1, 99, 99, 99, 99, 99, 42, 42, 6, 1, 1, 28, 1, 1, 2, 2, 2] 156 rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 33, 36, 37, 38]) total number of confs: 307 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042496 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042496 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042496/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042496 Building REAL250005042497 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042497' /scratch/stefan/7921153/working/building/REAL250005042497 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042497 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042497/0 /scratch/stefan/7921153/working/building/REAL250005042497 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 606) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/606 `/scratch/stefan/7921153/working/3D/606' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)=CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005042497.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042497/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042497 none CC(C)=CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 5, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 49, 49, 49, 23, 23, 23, 23, 10, 1, 10, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 68, 68, 68, 68, 68, 68, 68, 49, 23, 23, 1, 23, 23, 23, 23, 23] 68 rigid atoms, others: [33, 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, 34, 35, 36, 37, 38]) total number of confs: 189 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042497 none CC(C)=CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 5, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [21, 21, 21, 5, 5, 5, 1, 1, 1, 1, 1, 1, 6, 6, 23, 23, 23, 23, 23, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 21, 5, 1, 1, 23, 1, 1, 2, 2, 2] 68 rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 33, 36, 37, 38]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042497 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042497 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042497/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042497 Building REAL250005042498 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042498' /scratch/stefan/7921153/working/building/REAL250005042498 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042498 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042498/0 /scratch/stefan/7921153/working/building/REAL250005042498 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 607) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/607 `/scratch/stefan/7921153/working/3D/607' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005042498.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042498/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042498 none CSCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 175 conformations in input total number of sets (complete confs): 175 using faster count positions algorithm for large data unique positions, atoms: [175, 162, 76, 76, 76, 28, 28, 28, 28, 9, 1, 9, 1, 1, 1, 1, 1, 1, 27, 27, 28, 27, 175, 175, 175, 162, 162, 76, 28, 28, 1, 27, 27, 28, 28, 28] 175 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35]) total number of confs: 618 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042498 none CSCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 175 conformations in input total number of sets (complete confs): 175 using faster count positions algorithm for large data unique positions, atoms: [103, 47, 6, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 27, 28, 28, 28, 28, 1, 1, 1, 1, 98, 103, 103, 47, 47, 6, 1, 1, 27, 1, 1, 2, 2, 2] 175 rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 28, 29, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 30, 33, 34, 35]) total number of confs: 292 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042498 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042498 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042498/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042498 Building REAL250005042499 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042499' /scratch/stefan/7921153/working/building/REAL250005042499 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042499 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042499/0 /scratch/stefan/7921153/working/building/REAL250005042499 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 608) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/608 `/scratch/stefan/7921153/working/3D/608' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005042499.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042499/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042499 none CCCCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 201, 184, 72, 72, 72, 29, 29, 29, 29, 10, 1, 10, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 200, 201, 201, 201, 201, 201, 201, 184, 184, 72, 29, 29, 1, 29, 29, 29, 29, 29] 201 rigid atoms, others: [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, 34, 36, 37, 38, 39, 40]) total number of confs: 764 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042499 none CCCCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 62, 41, 6, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 29, 29, 29, 29, 29, 1, 1, 1, 1, 104, 107, 107, 102, 101, 75, 75, 41, 41, 6, 1, 1, 29, 1, 1, 2, 2, 2] 201 rigid atoms, others: [33, 34, 36, 37, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 38, 39, 40]) total number of confs: 595 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042499 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042499 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042499/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042499 Building REAL250005042500 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042500' /scratch/stefan/7921153/working/building/REAL250005042500 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042500 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042500/0 /scratch/stefan/7921153/working/building/REAL250005042500 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 609) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/609 `/scratch/stefan/7921153/working/3D/609' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005042500.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042500.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042500/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042500 none CC(C)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 48, 67, 48, 48, 26, 26, 26, 26, 10, 1, 10, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 67, 67, 67, 67, 67, 67, 67, 48, 26, 26, 1, 26, 26, 26, 26, 26] 67 rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37]) total number of confs: 230 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042500 none CC(C)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [29, 6, 29, 6, 6, 1, 1, 1, 1, 1, 1, 5, 5, 26, 25, 26, 26, 26, 1, 1, 1, 1, 29, 29, 29, 29, 29, 29, 29, 6, 1, 1, 26, 1, 1, 2, 2, 2] 67 rigid atoms, others: [33, 34, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 32, 35, 36, 37]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042500 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042500 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042500/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042500 Building REAL250005042501 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042501' /scratch/stefan/7921153/working/building/REAL250005042501 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042501 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042501/0 /scratch/stefan/7921153/working/building/REAL250005042501 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 610) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/610 `/scratch/stefan/7921153/working/3D/610' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005042501.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042501/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042501 none CCC(C)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [123, 122, 62, 122, 62, 62, 26, 26, 26, 26, 9, 1, 9, 1, 1, 1, 1, 1, 1, 25, 25, 26, 25, 123, 123, 123, 123, 123, 122, 122, 122, 122, 62, 26, 26, 1, 25, 25, 26, 26, 26] 123 rigid atoms, others: [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, 34, 36, 37, 38, 39, 40]) total number of confs: 449 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042501 none CCC(C)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [50, 37, 6, 37, 6, 6, 1, 1, 1, 1, 1, 1, 5, 5, 25, 26, 26, 26, 26, 1, 1, 1, 1, 53, 53, 53, 53, 53, 37, 37, 37, 37, 6, 1, 1, 25, 1, 1, 2, 2, 2] 123 rigid atoms, others: [33, 34, 36, 37, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 38, 39, 40]) total number of confs: 277 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042501 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042501 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042501/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042501 Building REAL250005042502 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042502' /scratch/stefan/7921153/working/building/REAL250005042502 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042502 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042502/0 /scratch/stefan/7921153/working/building/REAL250005042502 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 611) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/611 `/scratch/stefan/7921153/working/3D/611' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005042502.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042502/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042502 none COC(C)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 59, 40, 59, 40, 40, 17, 17, 18, 17, 9, 1, 9, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 60, 60, 60, 59, 59, 59, 59, 40, 18, 18, 1, 18, 18, 18, 18, 18] 60 rigid atoms, others: [33, 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, 34, 35, 36, 37, 38]) total number of confs: 199 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042502 none COC(C)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [37, 30, 6, 31, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 18, 18, 18, 18, 18, 1, 1, 1, 1, 37, 37, 37, 31, 31, 31, 31, 6, 1, 1, 18, 1, 1, 2, 2, 2] 60 rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 33, 36, 37, 38]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042502 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042502 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042502/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042502 Building REAL250005042503 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042503' /scratch/stefan/7921153/working/building/REAL250005042503 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042503 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042503/0 /scratch/stefan/7921153/working/building/REAL250005042503 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 612) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/612 `/scratch/stefan/7921153/working/3D/612' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005042503.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042503/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042503 none C=CCCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 179, 64, 64, 64, 24, 24, 24, 24, 8, 1, 8, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 201, 201, 201, 201, 201, 179, 179, 64, 24, 24, 1, 24, 24, 24, 24, 24] 201 rigid atoms, others: [33, 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, 34, 35, 36, 37, 38]) total number of confs: 767 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042503 none C=CCCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 77, 40, 6, 6, 6, 1, 1, 1, 1, 1, 1, 7, 7, 24, 24, 24, 24, 24, 1, 1, 1, 1, 126, 126, 126, 77, 77, 40, 40, 6, 1, 1, 24, 1, 1, 2, 2, 2] 201 rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 33, 36, 37, 38]) total number of confs: 541 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042503 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042503 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042503/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042503 Building REAL250005042504 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042504' /scratch/stefan/7921153/working/building/REAL250005042504 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042504 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042504/0 /scratch/stefan/7921153/working/building/REAL250005042504 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 613) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/613 `/scratch/stefan/7921153/working/3D/613' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=C(C)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005042504.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042504.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042504/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042504 none CC=C(C)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 43, 71, 43, 43, 22, 22, 22, 22, 10, 1, 10, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 71, 71, 71, 71, 71, 71, 71, 43, 22, 22, 1, 22, 22, 22, 22, 22] 71 rigid atoms, others: [33, 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, 34, 35, 36, 37, 38]) total number of confs: 196 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042504 none CC=C(C)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [38, 38, 6, 38, 6, 6, 1, 1, 1, 1, 1, 1, 5, 5, 22, 22, 22, 22, 22, 1, 1, 1, 1, 38, 38, 38, 38, 38, 38, 38, 6, 1, 1, 22, 1, 1, 2, 2, 2] 71 rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 33, 36, 37, 38]) total number of confs: 124 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042504 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042504 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042504/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042504 Building REAL250005042505 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042505' /scratch/stefan/7921153/working/building/REAL250005042505 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042505 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042505/0 /scratch/stefan/7921153/working/building/REAL250005042505 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 614) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/614 `/scratch/stefan/7921153/working/3D/614' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C1(C)CC1) `REAL250005042505.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042505.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042505/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042505 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C1(C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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] 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: [23, 23, 23, 23, 23, 23, 65, 65, 78, 78, 78, 78, 78, 23, 6, 23, 6, 1, 6, 1, 1, 1, 1, 23, 23, 23, 23, 23, 78, 23, 23, 6, 2, 2, 2, 1, 1, 1, 1] 78 rigid atoms, others: [35, 36, 37, 38, 17, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 212 number of broken/clashed sets: 4 ./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: REAL250005042505 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C1(C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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] 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: [26, 26, 26, 26, 7, 1, 7, 1, 1, 1, 1, 1, 1, 25, 25, 26, 25, 48, 48, 48, 78, 78, 78, 26, 26, 26, 26, 26, 1, 25, 25, 48, 78, 78, 78, 78, 78, 78, 78] 78 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 236 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042505 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C1(C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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] 0 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 25, 25, 26, 26, 26, 1, 1, 1, 1, 5, 5, 5, 23, 23, 23, 2, 2, 2, 1, 1, 25, 1, 1, 5, 23, 23, 23, 23, 23, 23, 23] 78 rigid atoms, others: [0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 26, 27, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 102 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042505 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042505 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042505/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042505 Building REAL250005042506 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042506' /scratch/stefan/7921153/working/building/REAL250005042506 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042506 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042506/0 /scratch/stefan/7921153/working/building/REAL250005042506 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 615) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/615 `/scratch/stefan/7921153/working/3D/615' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H]1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005042506.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042506.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042506/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042506 none C[C@@H]1C[C@H]1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [80, 80, 80, 80, 42, 80, 42, 42, 21, 21, 21, 21, 8, 1, 8, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 80, 80, 80, 80, 80, 42, 21, 21, 1, 21, 21, 21, 21, 21] 80 rigid atoms, others: [33, 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, 34, 35, 36, 37, 38]) total number of confs: 223 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: REAL250005042506 none C[C@@H]1C[C@H]1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 32, 32, 6, 32, 6, 6, 1, 1, 1, 1, 1, 1, 5, 5, 21, 21, 21, 21, 21, 1, 1, 1, 1, 32, 32, 32, 32, 32, 6, 1, 1, 21, 1, 1, 2, 2, 2] 80 rigid atoms, others: [32, 34, 35, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 33, 36, 37, 38]) total number of confs: 112 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042506 none C[C@@H]1C[C@H]1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 32, 32, 32, 32, 67, 67, 80, 80, 80, 80, 80, 32, 32, 32, 32, 2, 2, 2, 1, 1, 12, 32, 32, 80, 32, 32, 32, 32, 32] 80 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042506 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042506 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042506/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042506 Building REAL250005042507 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042507' /scratch/stefan/7921153/working/building/REAL250005042507 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042507 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042507/0 /scratch/stefan/7921153/working/building/REAL250005042507 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 616) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/616 `/scratch/stefan/7921153/working/3D/616' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(F)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005042507.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042507/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042507 none CCC(F)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 126, 75, 126, 75, 75, 31, 31, 31, 31, 10, 1, 10, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 138, 138, 138, 138, 138, 126, 75, 31, 31, 1, 31, 31, 31, 31, 31] 138 rigid atoms, others: [32, 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, 33, 34, 35, 36, 37]) total number of confs: 500 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042507 none CCC(F)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [60, 41, 6, 41, 6, 6, 1, 1, 1, 1, 1, 1, 7, 7, 31, 31, 31, 31, 31, 1, 1, 1, 1, 70, 70, 70, 70, 70, 41, 6, 1, 1, 31, 1, 1, 2, 2, 2] 138 rigid atoms, others: [33, 34, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 32, 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 /scratch/stefan/7921153/working/building/REAL250005042507 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042507 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042507/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042507 Building REAL250005042508 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042508' /scratch/stefan/7921153/working/building/REAL250005042508 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042508 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042508/0 /scratch/stefan/7921153/working/building/REAL250005042508 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 617) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/617 `/scratch/stefan/7921153/working/3D/617' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)CCCF) `REAL250005042508.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042508.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042508/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042508 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)CCCF NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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] 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: [20, 20, 20, 20, 6, 1, 6, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 54, 54, 54, 132, 134, 148, 20, 20, 20, 20, 20, 1, 20, 20, 54, 132, 132, 148, 148, 148, 148] 148 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 653 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042508 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)CCCF NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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] 0 hydrogens need rotated 148 conformations in input total number of sets (complete confs): 148 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 20, 20, 20, 20, 20, 1, 1, 1, 1, 6, 6, 6, 38, 44, 96, 2, 2, 2, 1, 1, 20, 1, 1, 6, 38, 38, 64, 64, 83, 88] 148 rigid atoms, others: [0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 26, 27, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 503 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042508 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042508 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042508/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042508 Building REAL250005042509 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042509' /scratch/stefan/7921153/working/building/REAL250005042509 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042509 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042509/0 /scratch/stefan/7921153/working/building/REAL250005042509 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 618) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/618 `/scratch/stefan/7921153/working/3D/618' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@@H]1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005042509.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042509.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042509/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042509 none C[C@H]1C[C@@H]1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 87 conformations in input total number of sets (complete confs): 87 using faster count positions algorithm for large data unique positions, atoms: [87, 87, 87, 87, 50, 87, 50, 50, 27, 27, 27, 26, 9, 1, 9, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 87, 87, 87, 87, 87, 50, 26, 26, 1, 27, 27, 27, 27, 27] 87 rigid atoms, others: [33, 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, 34, 35, 36, 37, 38]) total number of confs: 235 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: REAL250005042509 none C[C@H]1C[C@@H]1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 87 conformations in input total number of sets (complete confs): 87 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 32, 32, 5, 32, 5, 5, 1, 1, 1, 1, 1, 1, 6, 6, 27, 27, 27, 27, 26, 1, 1, 1, 1, 32, 32, 32, 32, 32, 5, 1, 1, 27, 1, 1, 2, 2, 2] 87 rigid atoms, others: [32, 34, 35, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 33, 36, 37, 38]) total number of confs: 119 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042509 none C[C@H]1C[C@@H]1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 87 conformations in input total number of sets (complete confs): 87 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 32, 32, 32, 32, 73, 73, 87, 87, 87, 87, 87, 32, 32, 32, 32, 2, 2, 2, 1, 1, 13, 32, 32, 87, 32, 32, 32, 32, 32] 87 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 241 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042509 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042509 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042509/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042509 Building REAL250005042510 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042510' /scratch/stefan/7921153/working/building/REAL250005042510 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042510 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042510/0 /scratch/stefan/7921153/working/building/REAL250005042510 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 619) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/619 `/scratch/stefan/7921153/working/3D/619' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C(N)=O) `REAL250005042510.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042510.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042510/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042510 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 4, 6, 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: [18, 18, 18, 18, 8, 1, 8, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 32, 32, 32, 38, 38, 18, 18, 18, 18, 18, 1, 18, 18, 32, 38, 38] 38 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 27] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32]) total number of confs: 99 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042510 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 18, 18, 18, 18, 18, 1, 1, 1, 1, 6, 6, 6, 14, 14, 2, 2, 2, 1, 1, 18, 1, 1, 6, 14, 14] 38 rigid atoms, others: [0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 25, 26, 28, 29] set([32, 6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 27, 30, 31]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042510 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042510 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042510/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042510 Building REAL250005042511 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042511' /scratch/stefan/7921153/working/building/REAL250005042511 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042511 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042511/0 /scratch/stefan/7921153/working/building/REAL250005042511 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 620) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/620 `/scratch/stefan/7921153/working/3D/620' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C(C)(C)C) `REAL250005042511.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042511/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042511 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 9, 1, 9, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 30, 30, 30, 32, 32, 32, 21, 21, 21, 21, 21, 1, 21, 21, 30, 32, 32, 32, 32, 32, 32, 32, 32, 32] 32 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 84 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042511 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 5, 21, 21, 21, 21, 21, 1, 1, 1, 1, 5, 5, 5, 9, 9, 9, 2, 2, 2, 1, 1, 21, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9] 32 rigid atoms, others: [0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 26, 27, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042511 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042511 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042511/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042511 Building REAL250005042512 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042512' /scratch/stefan/7921153/working/building/REAL250005042512 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042512 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042512/0 /scratch/stefan/7921153/working/building/REAL250005042512 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 621) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/621 `/scratch/stefan/7921153/working/3D/621' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005042512.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042512/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042512 none C=CCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 109 conformations in input total number of sets (complete confs): 109 using faster count positions algorithm for large data unique positions, atoms: [109, 109, 67, 67, 67, 26, 26, 26, 26, 9, 1, 9, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 109, 109, 109, 109, 109, 67, 26, 26, 1, 26, 26, 26, 26, 26] 109 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35]) total number of confs: 389 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042512 none C=CCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 109 conformations in input total number of sets (complete confs): 109 using faster count positions algorithm for large data unique positions, atoms: [72, 41, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 26, 26, 26, 26, 26, 1, 1, 1, 1, 72, 72, 72, 41, 41, 5, 1, 1, 26, 1, 1, 2, 2, 2] 109 rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 28, 29, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 30, 33, 34, 35]) total number of confs: 282 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042512 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042512 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042512/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042512 Building REAL250005042513 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042513' /scratch/stefan/7921153/working/building/REAL250005042513 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005042513 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042513/0 /scratch/stefan/7921153/working/building/REAL250005042513 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 622) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/622 `/scratch/stefan/7921153/working/3D/622' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C[NH+](C)C) `REAL250005042513.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042513.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042513/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042513 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C[NH+](C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 7, 1, 7, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 23, 23, 23, 30, 30, 30, 30, 10, 10, 10, 10, 10, 1, 10, 10, 23, 30, 30, 30, 30, 30, 30, 30, 30] 30 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 99 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042513 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C[NH+](C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 3, 3, 10, 10, 10, 10, 10, 1, 1, 1, 1, 6, 6, 6, 22, 24, 24, 24, 2, 2, 2, 1, 1, 10, 1, 1, 6, 22, 22, 24, 24, 24, 24, 24, 24] 30 rigid atoms, others: [0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 27, 28, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042513 /scratch/stefan/7921153/working /scratch/stefan/7921153 mkdir: created directory `1' /scratch/stefan/7921153/working/building/REAL250005042513/1 /scratch/stefan/7921153/working/building/REAL250005042513 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 1 (index: 623) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/623 `/scratch/stefan/7921153/working/3D/623' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)CN(C)C) `REAL250005042513.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005042513.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042513/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042513 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)CN(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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, 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: [24, 24, 24, 24, 10, 1, 10, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 57, 57, 57, 93, 95, 95, 24, 24, 24, 24, 24, 1, 24, 24, 57, 93, 93, 95, 95, 95, 95, 95, 95] 95 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 322 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042513 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)CN(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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, 7] 0 hydrogens need rotated 95 conformations in input total number of sets (complete confs): 95 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 24, 24, 24, 24, 24, 1, 1, 1, 1, 6, 6, 6, 33, 42, 42, 2, 2, 2, 1, 1, 24, 1, 1, 6, 33, 33, 42, 42, 42, 42, 42, 42] 95 rigid atoms, others: [0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 26, 27, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042513 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042513 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 1: /scratch/stefan/7921153/working/building/REAL250005042513/1.* 0: /scratch/stefan/7921153/working/building/REAL250005042513/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042513 Building REAL250005042514 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042514' /scratch/stefan/7921153/working/building/REAL250005042514 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042514 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042514/0 /scratch/stefan/7921153/working/building/REAL250005042514 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 624) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/624 `/scratch/stefan/7921153/working/3D/624' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(O)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005042514.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042514.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042514/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042514 none C=CC(O)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 321 conformations in input total number of sets (complete confs): 321 using faster count positions algorithm for large data unique positions, atoms: [107, 107, 61, 107, 61, 61, 25, 25, 25, 25, 9, 1, 9, 1, 1, 1, 1, 1, 1, 24, 24, 25, 24, 107, 107, 107, 107, 321, 61, 25, 25, 1, 24, 24, 25, 25, 25] 321 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 31] 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, 32, 33, 34, 35, 36]) total number of confs: 703 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042514 none C=CC(O)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 321 conformations in input total number of sets (complete confs): 321 using faster count positions algorithm for large data unique positions, atoms: [53, 35, 6, 35, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 24, 24, 25, 25, 25, 1, 1, 1, 1, 53, 53, 53, 35, 105, 6, 1, 1, 24, 1, 1, 2, 2, 2] 321 rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 29, 30] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 31, 34, 35, 36]) total number of confs: 327 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042514 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042514 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042514/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042514 Building REAL250005042515 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042515' /scratch/stefan/7921153/working/building/REAL250005042515 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042515 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042515/0 /scratch/stefan/7921153/working/building/REAL250005042515 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 625) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/625 `/scratch/stefan/7921153/working/3D/625' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C1COC1) `REAL250005042515.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042515.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042515/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042515 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C1COC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 3, 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: [36, 36, 36, 36, 36, 36, 64, 64, 70, 70, 70, 70, 70, 36, 13, 36, 13, 1, 13, 1, 1, 1, 1, 36, 36, 36, 36, 36, 70, 36, 36, 13, 1, 1, 1, 1, 1] 70 rigid atoms, others: [32, 33, 34, 35, 36, 17, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 203 number of broken/clashed sets: 3 ./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: REAL250005042515 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C1COC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 3, 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: [18, 18, 18, 18, 9, 1, 9, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 39, 39, 39, 70, 70, 70, 18, 18, 18, 18, 18, 1, 18, 18, 39, 70, 70, 70, 70, 70] 70 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 191 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042515 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C1COC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 5, 18, 18, 18, 18, 18, 1, 1, 1, 1, 6, 6, 6, 36, 36, 36, 2, 2, 2, 1, 1, 18, 1, 1, 6, 36, 36, 36, 36, 36] 70 rigid atoms, others: [0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 26, 27, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 31, 32, 33, 34, 35, 36]) total number of confs: 115 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042515 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042515 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042515/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042515 Building REAL250005042516 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042516' /scratch/stefan/7921153/working/building/REAL250005042516 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042516 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042516/0 /scratch/stefan/7921153/working/building/REAL250005042516 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 626) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/626 `/scratch/stefan/7921153/working/3D/626' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H](C)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005042516.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042516/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042516 none CO[C@H](C)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 54, 70, 70, 54, 54, 25, 25, 25, 25, 9, 1, 9, 1, 1, 1, 1, 1, 1, 24, 24, 25, 24, 70, 70, 70, 70, 70, 70, 54, 25, 25, 1, 24, 24, 25, 25, 25] 70 rigid atoms, others: [33, 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, 34, 35, 36, 37, 38]) total number of confs: 223 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042516 none CO[C@H](C)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [40, 30, 6, 31, 31, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 24, 25, 25, 25, 25, 1, 1, 1, 1, 40, 40, 40, 31, 31, 31, 6, 1, 1, 24, 1, 1, 2, 2, 2] 70 rigid atoms, others: [32, 34, 35, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 33, 36, 37, 38]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042516 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042516 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042516/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042516 Building REAL250005042517 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042517' /scratch/stefan/7921153/working/building/REAL250005042517 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042517 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042517/0 /scratch/stefan/7921153/working/building/REAL250005042517 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 627) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/627 `/scratch/stefan/7921153/working/3D/627' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC=CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005042517.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042517.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042517/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042517 none CCC=CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 91, 91, 63, 63, 63, 27, 27, 27, 27, 10, 1, 10, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 119, 119, 119, 119, 119, 91, 91, 63, 27, 27, 1, 27, 27, 27, 27, 27] 119 rigid atoms, others: [33, 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, 34, 35, 36, 37, 38]) total number of confs: 435 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042517 none CCC=CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [56, 31, 31, 5, 5, 5, 1, 1, 1, 1, 1, 1, 6, 6, 27, 27, 27, 27, 27, 1, 1, 1, 1, 56, 56, 56, 56, 56, 31, 31, 5, 1, 1, 27, 1, 1, 2, 2, 2] 119 rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 33, 36, 37, 38]) total number of confs: 251 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042517 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042517 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042517/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042517 Building REAL250005042518 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042518' /scratch/stefan/7921153/working/building/REAL250005042518 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042518 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042518/0 /scratch/stefan/7921153/working/building/REAL250005042518 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 628) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/628 `/scratch/stefan/7921153/working/3D/628' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)CN=[N+]=[N-]) `REAL250005042518.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042518.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042518/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042518 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)CN=[N+]=[N-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.2', 'N.1', 'N.1', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 26, 26, 8, 1, 8, 1, 1, 1, 1, 1, 1, 25, 25, 26, 25, 69, 69, 69, 188, 201, 201, 26, 26, 26, 26, 26, 1, 25, 25, 69, 188, 188] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33]) total number of confs: 680 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042518 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)CN=[N+]=[N-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.2', 'N.1', 'N.1', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 7, 26, 26, 26, 26, 26, 1, 1, 1, 1, 5, 5, 5, 48, 145, 145, 2, 2, 2, 1, 1, 26, 1, 1, 5, 48, 48] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 26, 27, 29, 30] set([32, 33, 6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 31]) total number of confs: 329 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042518 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042518 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042518/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042518 Building REAL250005042519 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042519' /scratch/stefan/7921153/working/building/REAL250005042519 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042519 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042519/0 /scratch/stefan/7921153/working/building/REAL250005042519 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 629) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/629 `/scratch/stefan/7921153/working/3D/629' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)CO) `REAL250005042519.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042519.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042519/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042519 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)CO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [22, 22, 22, 22, 8, 1, 8, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 40, 40, 40, 41, 22, 22, 22, 22, 22, 1, 22, 22, 40, 41, 41, 123] 123 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 26] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32]) total number of confs: 232 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042519 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)CO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 7, 22, 22, 22, 22, 22, 1, 1, 1, 1, 6, 6, 6, 20, 2, 2, 2, 1, 1, 22, 1, 1, 6, 20, 20, 60] 123 rigid atoms, others: [0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 24, 25, 27, 28] set([32, 6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 26, 29, 30, 31]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042519 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042519 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042519/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042519 Building REAL250005042520 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042520' /scratch/stefan/7921153/working/building/REAL250005042520 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042520 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042520/0 /scratch/stefan/7921153/working/building/REAL250005042520 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 630) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/630 `/scratch/stefan/7921153/working/3D/630' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005042520.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042520.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042520/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042520 none CC(O)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [50, 39, 50, 39, 39, 25, 25, 26, 25, 9, 1, 9, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 50, 50, 50, 50, 150, 39, 25, 25, 1, 26, 26, 26, 26, 26] 150 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35]) total number of confs: 298 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042520 none CC(O)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [25, 6, 25, 6, 6, 1, 1, 1, 1, 1, 1, 6, 7, 26, 26, 26, 26, 26, 1, 1, 1, 1, 25, 25, 25, 25, 75, 6, 1, 1, 26, 1, 1, 2, 2, 2] 150 rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 28, 29, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 30, 33, 34, 35]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042520 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042520 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042520/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042520 Building REAL250005042521 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042521' /scratch/stefan/7921153/working/building/REAL250005042521 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042521 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042521/0 /scratch/stefan/7921153/working/building/REAL250005042521 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 631) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/631 `/scratch/stefan/7921153/working/3D/631' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C1CC1F) `REAL250005042521.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042521.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042521/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042521 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C1CC1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 79 conformations in input total number of sets (complete confs): 79 using faster count positions algorithm for large data unique positions, atoms: [31, 31, 31, 31, 31, 31, 73, 73, 79, 79, 79, 79, 79, 31, 12, 31, 12, 1, 12, 1, 1, 1, 1, 31, 31, 31, 31, 31, 79, 31, 31, 12, 1, 1, 1, 1] 79 rigid atoms, others: [32, 33, 34, 35, 17, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 229 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: REAL250005042521 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C1CC1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 79 conformations in input total number of sets (complete confs): 79 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 24, 24, 10, 1, 10, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 46, 46, 46, 79, 79, 79, 24, 24, 24, 24, 24, 1, 24, 24, 46, 79, 79, 79, 79] 79 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 214 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042521 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C1CC1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 79 conformations in input total number of sets (complete confs): 79 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 24, 24, 24, 24, 24, 1, 1, 1, 1, 5, 5, 5, 31, 31, 31, 2, 2, 2, 1, 1, 24, 1, 1, 5, 31, 31, 31, 31] 79 rigid atoms, others: [0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 26, 27, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 31, 32, 33, 34, 35]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042521 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042521 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042521/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042521 Building REAL250005042522 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042522' /scratch/stefan/7921153/working/building/REAL250005042522 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042522 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042522/0 /scratch/stefan/7921153/working/building/REAL250005042522 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 632) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/632 `/scratch/stefan/7921153/working/3D/632' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)CCF) `REAL250005042522.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042522.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042522/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042522 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)CCF NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 121 conformations in input total number of sets (complete confs): 121 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 28, 28, 10, 1, 10, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 66, 66, 66, 121, 121, 28, 28, 28, 28, 28, 1, 28, 28, 66, 121, 121, 121, 121] 121 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 27] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 421 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042522 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)CCF NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 121 conformations in input total number of sets (complete confs): 121 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 28, 28, 28, 28, 28, 1, 1, 1, 1, 5, 5, 5, 34, 62, 2, 2, 2, 1, 1, 28, 1, 1, 5, 34, 34, 62, 62] 121 rigid atoms, others: [0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 25, 26, 28, 29] set([32, 33, 34, 6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 27, 30, 31]) total number of confs: 306 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042522 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042522 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042522/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042522 Building REAL250005042523 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042523' /scratch/stefan/7921153/working/building/REAL250005042523 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042523 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042523/0 /scratch/stefan/7921153/working/building/REAL250005042523 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 633) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/633 `/scratch/stefan/7921153/working/3D/633' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C=CCF) `REAL250005042523.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042523.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042523/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042523 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C=CCF NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 1, 1, 5, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 97 conformations in input total number of sets (complete confs): 97 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 25, 25, 9, 1, 9, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 62, 62, 62, 97, 97, 97, 25, 25, 25, 25, 25, 1, 25, 25, 62, 97, 97, 97, 97] 97 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 279 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042523 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C=CCF NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 1, 1, 5, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 97 conformations in input total number of sets (complete confs): 97 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 5, 25, 25, 25, 25, 25, 1, 1, 1, 1, 6, 6, 6, 32, 32, 62, 2, 2, 2, 1, 1, 25, 1, 1, 6, 32, 32, 62, 62] 97 rigid atoms, others: [0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 26, 27, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 31, 32, 33, 34, 35]) total number of confs: 249 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042523 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042523 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042523/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042523 Building REAL250005042524 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042524' /scratch/stefan/7921153/working/building/REAL250005042524 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042524 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042524/0 /scratch/stefan/7921153/working/building/REAL250005042524 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 634) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/634 `/scratch/stefan/7921153/working/3D/634' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005042524.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042524/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042524 none C#CCCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 145 conformations in input total number of sets (complete confs): 145 using faster count positions algorithm for large data unique positions, atoms: [145, 145, 135, 66, 66, 66, 29, 29, 29, 29, 10, 1, 10, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 145, 145, 145, 135, 135, 66, 29, 29, 1, 29, 29, 29, 29, 29] 145 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 31] 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, 32, 33, 34, 35, 36]) total number of confs: 529 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042524 none C#CCCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 145 conformations in input total number of sets (complete confs): 145 using faster count positions algorithm for large data unique positions, atoms: [68, 68, 38, 6, 6, 6, 1, 1, 1, 1, 1, 1, 7, 7, 29, 29, 29, 29, 29, 1, 1, 1, 1, 68, 68, 68, 38, 38, 6, 1, 1, 29, 1, 1, 2, 2, 2] 145 rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 29, 30] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 31, 34, 35, 36]) total number of confs: 337 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042524 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042524 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042524/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042524 Building REAL250005042525 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042525' /scratch/stefan/7921153/working/building/REAL250005042525 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042525 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042525/0 /scratch/stefan/7921153/working/building/REAL250005042525 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 635) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/635 `/scratch/stefan/7921153/working/3D/635' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C1CCO1) `REAL250005042525.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042525.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042525/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042525 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C1CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 23, 23, 38, 38, 42, 42, 42, 42, 42, 23, 11, 23, 11, 1, 11, 1, 1, 1, 1, 23, 23, 23, 23, 23, 42, 23, 23, 11, 1, 1, 1, 1, 1] 42 rigid atoms, others: [32, 33, 34, 35, 36, 17, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 118 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: REAL250005042525 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C1CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 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: [21, 21, 21, 21, 9, 1, 9, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 33, 33, 33, 42, 42, 42, 21, 21, 21, 21, 21, 1, 21, 21, 33, 42, 42, 42, 42, 42] 42 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 109 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042525 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C1CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 7, 21, 21, 21, 21, 21, 1, 1, 1, 1, 6, 6, 6, 23, 23, 23, 2, 2, 2, 1, 1, 21, 1, 1, 6, 23, 23, 23, 23, 23] 42 rigid atoms, others: [0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 26, 27, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 31, 32, 33, 34, 35, 36]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042525 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042525 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042525/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042525 Building REAL250005042526 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042526' /scratch/stefan/7921153/working/building/REAL250005042526 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042526 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042526/0 /scratch/stefan/7921153/working/building/REAL250005042526 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 636) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/636 `/scratch/stefan/7921153/working/3D/636' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C(C)(C)O) `REAL250005042526.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042526.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042526/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042526 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C(C)(C)O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 210 conformations in input total number of sets (complete confs): 210 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 26, 26, 10, 1, 10, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 56, 56, 56, 70, 70, 70, 26, 26, 26, 26, 26, 1, 26, 26, 56, 70, 70, 70, 70, 70, 70, 210] 210 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 421 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042526 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C(C)(C)O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 210 conformations in input total number of sets (complete confs): 210 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 26, 26, 26, 26, 26, 1, 1, 1, 1, 6, 6, 6, 29, 29, 28, 2, 2, 2, 1, 1, 26, 1, 1, 6, 29, 29, 29, 29, 29, 29, 87] 210 rigid atoms, others: [0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 26, 27, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042526 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042526 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042526/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042526 Building REAL250005042527 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042527' /scratch/stefan/7921153/working/building/REAL250005042527 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042527 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042527/0 /scratch/stefan/7921153/working/building/REAL250005042527 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 637) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/637 `/scratch/stefan/7921153/working/3D/637' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005042527.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042527.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042527/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042527 none CC1=CC1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 52, 52, 52, 28, 28, 28, 28, 10, 1, 10, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 100, 100, 100, 100, 100, 52, 28, 28, 1, 28, 28, 28, 28, 28] 100 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 31] 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, 32, 33, 34, 35, 36]) total number of confs: 270 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: REAL250005042527 none CC1=CC1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [45, 45, 45, 6, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 28, 28, 28, 28, 28, 1, 1, 1, 1, 45, 45, 45, 45, 45, 6, 1, 1, 28, 1, 1, 2, 2, 2] 100 rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 29, 30] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 31, 34, 35, 36]) total number of confs: 147 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042527 none CC1=CC1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 13, 13, 13, 45, 45, 45, 45, 82, 82, 100, 100, 100, 100, 100, 45, 45, 45, 45, 2, 2, 2, 1, 1, 13, 45, 45, 100, 45, 45, 45, 45, 45] 100 rigid atoms, others: [0, 1, 2, 3, 4, 26, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 281 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042527 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042527 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042527/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042527 Building REAL250005042528 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042528' /scratch/stefan/7921153/working/building/REAL250005042528 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042528 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042528/0 /scratch/stefan/7921153/working/building/REAL250005042528 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 638) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/638 `/scratch/stefan/7921153/working/3D/638' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](O)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005042528.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042528.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042528/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042528 none C[C@@H](O)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [50, 39, 50, 50, 39, 39, 26, 26, 26, 26, 9, 1, 9, 1, 1, 1, 1, 1, 1, 25, 25, 26, 25, 50, 50, 50, 150, 39, 26, 26, 1, 25, 25, 26, 26, 26] 150 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35]) total number of confs: 300 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042528 none C[C@@H](O)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [25, 6, 25, 25, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 25, 26, 26, 26, 26, 1, 1, 1, 1, 25, 25, 25, 75, 6, 1, 1, 25, 1, 1, 2, 2, 2] 150 rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 28, 29, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 30, 33, 34, 35]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042528 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042528 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042528/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042528 Building REAL250005042529 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042529' /scratch/stefan/7921153/working/building/REAL250005042529 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042529 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042529/0 /scratch/stefan/7921153/working/building/REAL250005042529 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 639) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/639 `/scratch/stefan/7921153/working/3D/639' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C=CCO) `REAL250005042529.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042529.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042529/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042529 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C=CCO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 1, 1, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 333 conformations in input total number of sets (complete confs): 333 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 26, 26, 10, 1, 10, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 62, 62, 62, 109, 109, 111, 26, 26, 26, 26, 26, 1, 26, 26, 62, 109, 109, 111, 111, 333] 333 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 653 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042529 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C=CCO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 1, 1, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 333 conformations in input total number of sets (complete confs): 333 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 26, 26, 26, 26, 26, 1, 1, 1, 1, 6, 6, 6, 35, 35, 73, 2, 2, 2, 1, 1, 26, 1, 1, 6, 35, 35, 73, 73, 219] 333 rigid atoms, others: [0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 26, 27, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 31, 32, 33, 34, 35, 36]) total number of confs: 506 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042529 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042529 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042529/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042529 Building REAL250005042530 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042530' /scratch/stefan/7921153/working/building/REAL250005042530 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042530 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042530/0 /scratch/stefan/7921153/working/building/REAL250005042530 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 640) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/640 `/scratch/stefan/7921153/working/3D/640' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C1=CCC1) `REAL250005042530.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042530.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042530/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042530 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C1=CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 12, 12, 12, 23, 23, 31, 31, 31, 31, 31, 12, 6, 12, 6, 1, 6, 1, 1, 1, 1, 12, 12, 12, 12, 12, 31, 12, 12, 6, 1, 1, 1, 1, 1] 31 rigid atoms, others: [32, 33, 34, 35, 36, 17, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 78 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: REAL250005042530 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C1=CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 7, 1, 7, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 31, 31, 31, 31, 31, 31, 19, 19, 19, 18, 18, 1, 18, 18, 31, 31, 31, 31, 31, 31] 31 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 84 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042530 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C1=CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 18, 18, 18, 18, 18, 1, 1, 1, 1, 5, 5, 5, 12, 12, 12, 2, 2, 2, 1, 1, 18, 1, 1, 5, 12, 12, 12, 12, 12] 31 rigid atoms, others: [0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 26, 27, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 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/7921153/working/building/REAL250005042530 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042530 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042530/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042530 Building REAL250005042531 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042531' /scratch/stefan/7921153/working/building/REAL250005042531 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042531 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042531/0 /scratch/stefan/7921153/working/building/REAL250005042531 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 641) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/641 `/scratch/stefan/7921153/working/3D/641' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CON=CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005042531.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042531.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042531/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042531 none CON=CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 8, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 30, 30, 30, 17, 17, 17, 17, 10, 1, 10, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 37, 37, 37, 37, 30, 17, 17, 1, 17, 17, 17, 17, 17] 37 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35]) total number of confs: 97 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042531 none CON=CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 8, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [26, 20, 20, 6, 6, 6, 1, 1, 1, 1, 1, 1, 5, 5, 17, 17, 17, 17, 17, 1, 1, 1, 1, 26, 26, 26, 20, 6, 1, 1, 17, 1, 1, 2, 2, 2] 37 rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 28, 29, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 30, 33, 34, 35]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042531 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042531 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042531/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042531 Building REAL250005042532 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042532' /scratch/stefan/7921153/working/building/REAL250005042532 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042532 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042532/0 /scratch/stefan/7921153/working/building/REAL250005042532 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 642) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/642 `/scratch/stefan/7921153/working/3D/642' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C1(F)CC1) `REAL250005042532.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042532.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042532/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042532 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C1(F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 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: [37, 37, 37, 37, 37, 37, 70, 70, 81, 81, 81, 81, 81, 37, 12, 37, 12, 1, 12, 1, 1, 1, 1, 37, 37, 37, 37, 37, 81, 37, 37, 12, 1, 1, 1, 1] 81 rigid atoms, others: [32, 33, 34, 35, 17, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 223 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: REAL250005042532 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C1(F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 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: [27, 27, 27, 26, 9, 1, 9, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 58, 58, 58, 81, 81, 81, 27, 27, 27, 26, 26, 1, 27, 27, 58, 81, 81, 81, 81] 81 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 217 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042532 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C1(F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 26, 26, 26, 26, 26, 1, 1, 1, 1, 6, 6, 6, 37, 37, 37, 2, 2, 2, 1, 1, 27, 1, 1, 6, 37, 37, 37, 37] 81 rigid atoms, others: [0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 26, 27, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 31, 32, 33, 34, 35]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042532 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042532 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042532/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042532 Building REAL250005042533 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042533' /scratch/stefan/7921153/working/building/REAL250005042533 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042533 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042533/0 /scratch/stefan/7921153/working/building/REAL250005042533 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 643) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/643 `/scratch/stefan/7921153/working/3D/643' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=C(F)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005042533.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042533.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042533/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042533 none CC=C(F)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 15, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 34, 41, 34, 34, 21, 21, 21, 21, 10, 1, 10, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 41, 41, 41, 41, 34, 21, 21, 1, 21, 21, 21, 21, 21] 41 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35]) total number of confs: 106 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042533 none CC=C(F)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 15, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 6, 21, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 21, 21, 21, 21, 21, 1, 1, 1, 1, 23, 23, 23, 23, 6, 1, 1, 21, 1, 1, 2, 2, 2] 41 rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 28, 29, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 30, 33, 34, 35]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042533 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042533 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042533/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042533 Building REAL250005042534 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042534' /scratch/stefan/7921153/working/building/REAL250005042534 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042534 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042534/0 /scratch/stefan/7921153/working/building/REAL250005042534 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 644) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/644 `/scratch/stefan/7921153/working/3D/644' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CO)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005042534.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042534/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042534 none CC(CO)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 333 conformations in input total number of sets (complete confs): 333 using faster count positions algorithm for large data unique positions, atoms: [110, 57, 110, 111, 57, 57, 23, 23, 23, 23, 9, 1, 9, 1, 1, 1, 1, 1, 1, 22, 22, 23, 22, 110, 110, 110, 110, 111, 111, 333, 57, 23, 23, 1, 22, 22, 23, 23, 23] 333 rigid atoms, others: [33, 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, 34, 35, 36, 37, 38]) total number of confs: 731 number of broken/clashed sets: 46 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042534 none CC(CO)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 333 conformations in input total number of sets (complete confs): 333 using faster count positions algorithm for large data unique positions, atoms: [38, 6, 38, 63, 6, 6, 1, 1, 1, 1, 1, 1, 5, 5, 22, 23, 23, 23, 23, 1, 1, 1, 1, 38, 38, 38, 38, 63, 63, 189, 6, 1, 1, 22, 1, 1, 2, 2, 2] 333 rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 33, 36, 37, 38]) total number of confs: 485 number of broken/clashed sets: 46 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042534 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042534 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042534/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042534 Building REAL250005042535 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042535' /scratch/stefan/7921153/working/building/REAL250005042535 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042535 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042535/0 /scratch/stefan/7921153/working/building/REAL250005042535 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 645) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/645 `/scratch/stefan/7921153/working/3D/645' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](O)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005042535.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042535.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042535/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042535 none C[C@H](O)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 147 conformations in input total number of sets (complete confs): 147 using faster count positions algorithm for large data unique positions, atoms: [49, 36, 49, 49, 36, 36, 23, 23, 23, 23, 9, 1, 9, 1, 1, 1, 1, 1, 1, 22, 22, 23, 22, 49, 49, 49, 147, 36, 23, 23, 1, 22, 22, 23, 23, 23] 147 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35]) total number of confs: 309 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042535 none C[C@H](O)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 147 conformations in input total number of sets (complete confs): 147 using faster count positions algorithm for large data unique positions, atoms: [30, 6, 30, 30, 6, 6, 1, 1, 1, 1, 1, 1, 5, 5, 22, 23, 23, 23, 23, 1, 1, 1, 1, 30, 30, 30, 90, 6, 1, 1, 22, 1, 1, 2, 2, 2] 147 rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 28, 29, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 30, 33, 34, 35]) total number of confs: 227 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042535 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042535 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042535/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042535 Building REAL250005042536 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042536' /scratch/stefan/7921153/working/building/REAL250005042536 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042536 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042536/0 /scratch/stefan/7921153/working/building/REAL250005042536 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 646) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/646 `/scratch/stefan/7921153/working/3D/646' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C1CC1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005042536.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042536.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042536/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042536 none C=C1CC1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 92 conformations in input total number of sets (complete confs): 92 using faster count positions algorithm for large data unique positions, atoms: [92, 92, 92, 48, 48, 48, 23, 23, 23, 23, 9, 1, 9, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 92, 92, 92, 92, 92, 48, 23, 23, 1, 23, 23, 23, 23, 23] 92 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 31] 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, 32, 33, 34, 35, 36]) total number of confs: 243 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: REAL250005042536 none C=C1CC1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 92 conformations in input total number of sets (complete confs): 92 using faster count positions algorithm for large data unique positions, atoms: [40, 40, 40, 6, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 23, 23, 23, 23, 23, 1, 1, 1, 1, 40, 40, 40, 40, 40, 6, 1, 1, 23, 1, 1, 2, 2, 2] 92 rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 29, 30] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 31, 34, 35, 36]) total number of confs: 131 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042536 none C=C1CC1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 92 conformations in input total number of sets (complete confs): 92 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 13, 13, 13, 40, 40, 40, 40, 75, 75, 92, 92, 92, 92, 92, 40, 40, 40, 40, 1, 1, 1, 1, 1, 13, 40, 40, 92, 40, 40, 40, 40, 40] 92 rigid atoms, others: [0, 1, 2, 3, 4, 23, 24, 25, 26, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 259 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042536 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042536 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042536/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042536 Building REAL250005042537 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042537' /scratch/stefan/7921153/working/building/REAL250005042537 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042537 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042537/0 /scratch/stefan/7921153/working/building/REAL250005042537 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 647) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/647 `/scratch/stefan/7921153/working/3D/647' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CF)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005042537.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042537.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042537/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042537 none CC(CF)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [115, 56, 115, 117, 56, 56, 22, 22, 22, 22, 9, 1, 9, 1, 1, 1, 1, 1, 1, 21, 21, 22, 21, 115, 115, 115, 115, 117, 117, 56, 22, 22, 1, 21, 21, 22, 22, 22] 117 rigid atoms, others: [32, 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, 33, 34, 35, 36, 37]) total number of confs: 431 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042537 none CC(CF)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [37, 6, 37, 73, 6, 6, 1, 1, 1, 1, 1, 1, 5, 5, 21, 22, 22, 22, 22, 1, 1, 1, 1, 37, 37, 37, 37, 73, 73, 6, 1, 1, 21, 1, 1, 2, 2, 2] 117 rigid atoms, others: [33, 34, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 32, 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/7921153/working/building/REAL250005042537 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042537 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042537/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042537 Building REAL250005042538 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042538' /scratch/stefan/7921153/working/building/REAL250005042538 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042538 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042538/0 /scratch/stefan/7921153/working/building/REAL250005042538 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 648) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/648 `/scratch/stefan/7921153/working/3D/648' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C(C)CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005042538.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042538.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042538/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042538 none C=C(C)CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 58, 58, 58, 26, 26, 26, 25, 9, 1, 9, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 111, 111, 111, 111, 111, 111, 111, 58, 25, 25, 1, 26, 26, 26, 26, 26] 111 rigid atoms, others: [33, 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, 34, 35, 36, 37, 38]) total number of confs: 388 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042538 none C=C(C)CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [60, 44, 60, 6, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 26, 26, 26, 26, 25, 1, 1, 1, 1, 60, 60, 60, 60, 60, 44, 44, 6, 1, 1, 26, 1, 1, 2, 2, 2] 111 rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 33, 36, 37, 38]) total number of confs: 244 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042538 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042538 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042538/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042538 Building REAL250005042539 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042539' /scratch/stefan/7921153/working/building/REAL250005042539 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042539 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042539/0 /scratch/stefan/7921153/working/building/REAL250005042539 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 649) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/649 `/scratch/stefan/7921153/working/3D/649' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005042539.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042539.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042539/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042539 none CC=CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 41, 41, 41, 23, 23, 23, 23, 10, 1, 10, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 50, 50, 50, 50, 50, 41, 23, 23, 1, 23, 23, 23, 23, 23] 50 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35]) total number of confs: 135 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042539 none CC=CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 6, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 23, 23, 23, 23, 23, 1, 1, 1, 1, 20, 20, 20, 20, 20, 6, 1, 1, 23, 1, 1, 2, 2, 2] 50 rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 28, 29, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 30, 33, 34, 35]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042539 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042539 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042539/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042539 Building REAL250005042540 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042540' /scratch/stefan/7921153/working/building/REAL250005042540 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042540 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042540/0 /scratch/stefan/7921153/working/building/REAL250005042540 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 650) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/650 `/scratch/stefan/7921153/working/3D/650' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H]1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005042540.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042540.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042540/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042540 none C[C@@H]1C[C@H]1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [80, 80, 80, 80, 42, 80, 42, 42, 21, 21, 21, 21, 8, 1, 8, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 80, 80, 80, 80, 80, 42, 21, 21, 1, 21, 21, 21, 21, 21] 80 rigid atoms, others: [33, 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, 34, 35, 36, 37, 38]) total number of confs: 223 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: REAL250005042540 none C[C@@H]1C[C@H]1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 32, 32, 6, 32, 6, 6, 1, 1, 1, 1, 1, 1, 5, 5, 21, 21, 21, 21, 21, 1, 1, 1, 1, 32, 32, 32, 32, 32, 6, 1, 1, 21, 1, 1, 2, 2, 2] 80 rigid atoms, others: [32, 34, 35, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 33, 36, 37, 38]) total number of confs: 112 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042540 none C[C@@H]1C[C@H]1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 32, 32, 32, 32, 67, 67, 80, 80, 80, 80, 80, 32, 32, 32, 32, 2, 2, 2, 1, 1, 12, 32, 32, 80, 32, 32, 32, 32, 32] 80 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042540 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042540 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042540/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042540 Building REAL250005042541 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042541' /scratch/stefan/7921153/working/building/REAL250005042541 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042541 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042541/0 /scratch/stefan/7921153/working/building/REAL250005042541 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 651) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/651 `/scratch/stefan/7921153/working/3D/651' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C1(O)CC1) `REAL250005042541.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042541.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042541/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042541 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C1(O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 225 conformations in input total number of sets (complete confs): 225 using faster count positions algorithm for large data unique positions, atoms: [34, 34, 34, 34, 34, 34, 61, 61, 75, 75, 75, 75, 75, 34, 11, 34, 11, 1, 11, 1, 1, 1, 1, 34, 34, 34, 34, 34, 75, 34, 34, 11, 6, 1, 1, 1, 1] 225 rigid atoms, others: [33, 34, 35, 36, 17, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 216 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: REAL250005042541 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C1(O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 225 conformations in input total number of sets (complete confs): 225 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 25, 24, 8, 1, 8, 1, 1, 1, 1, 1, 1, 24, 25, 25, 25, 57, 57, 57, 75, 75, 75, 25, 25, 25, 24, 24, 1, 24, 24, 57, 225, 75, 75, 75, 75] 225 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 430 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042541 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C1(O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 225 conformations in input total number of sets (complete confs): 225 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 24, 24, 25, 24, 24, 1, 1, 1, 1, 5, 5, 5, 34, 34, 34, 2, 2, 2, 1, 1, 24, 1, 1, 5, 102, 34, 34, 34, 34] 225 rigid atoms, others: [0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 26, 27, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 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/7921153/working/building/REAL250005042541 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042541 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042541/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042541 Building REAL250005042542 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042542' /scratch/stefan/7921153/working/building/REAL250005042542 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042542 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042542/0 /scratch/stefan/7921153/working/building/REAL250005042542 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 652) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/652 `/scratch/stefan/7921153/working/3D/652' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)CC2CC2)C[C@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005042542.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042542.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042542/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042542 none C[C@@H]1CN(C(=O)CC2CC2)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 17, 17, 17, 17, 37, 37, 61, 69, 69, 17, 9, 17, 9, 1, 9, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 61, 61, 69, 69, 69, 69, 69, 17, 17, 9, 1] 69 rigid atoms, others: [38, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 250 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: REAL250005042542 none C[C@@H]1CN(C(=O)CC2CC2)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 35, 35, 14, 3, 14, 1, 1, 1, 1, 35, 35, 35, 35, 65, 65, 65, 69, 69, 69, 69, 69, 35, 35, 35, 35, 35, 3, 3, 1, 1, 1, 1, 1, 35, 35, 65, 69] 69 rigid atoms, others: [32, 33, 34, 7, 8, 9, 10, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38]) total number of confs: 176 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042542 none C[C@@H]1CN(C(=O)CC2CC2)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 27, 35, 35, 1, 1, 1, 1, 6, 6, 6, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 27, 27, 35, 35, 35, 35, 35, 1, 1, 6, 17] 69 rigid atoms, others: [0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 35, 36, 26, 27] set([6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 37, 38]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042542 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042542 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042542/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042542 Building REAL250005042543 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042543' /scratch/stefan/7921153/working/building/REAL250005042543 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042543 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042543/0 /scratch/stefan/7921153/working/building/REAL250005042543 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 653) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/653 `/scratch/stefan/7921153/working/3D/653' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C(C)(C)F)C[C@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005042543.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042543.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042543/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042543 none C[C@@H]1CN(C(=O)C(C)(C)F)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 15, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 10, 17, 17, 21, 21, 21, 10, 6, 10, 6, 1, 6, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 21, 21, 21, 21, 21, 21, 10, 10, 6, 1] 21 rigid atoms, others: [37, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 71 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042543 none C[C@@H]1CN(C(=O)C(C)(C)F)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 15, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 12, 12, 12, 1, 1, 1, 1, 6, 6, 6, 10, 10, 10, 10, 10, 2, 2, 2, 1, 1, 12, 12, 12, 12, 12, 12, 1, 1, 6, 10] 21 rigid atoms, others: [0, 1, 2, 3, 4, 5, 11, 12, 34, 14, 13, 35, 26, 27] set([6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 36, 37]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042543 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042543 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042543/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042543 Building REAL250005042544 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042544' /scratch/stefan/7921153/working/building/REAL250005042544 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042544 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042544/0 /scratch/stefan/7921153/working/building/REAL250005042544 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 654) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/654 `/scratch/stefan/7921153/working/3D/654' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042544.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042544.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042544/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042544 none COCC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 55, 30, 17, 30, 17, 17, 17, 17, 17, 7, 17, 7, 1, 7, 1, 1, 1, 1, 1, 1, 17, 58, 58, 58, 55, 55, 17, 17, 17, 17, 17, 7, 1, 17, 17] 58 rigid atoms, others: [33, 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, 34, 35]) total number of confs: 211 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042544 none COCC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [39, 23, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 17, 17, 17, 17, 17, 1, 40, 40, 40, 23, 23, 1, 1, 2, 2, 2, 6, 17, 1, 1] 58 rigid atoms, others: [34, 3, 5, 6, 7, 8, 9, 10, 11, 12, 35, 21, 27, 28] set([0, 1, 2, 4, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042544 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042544 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042544/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042544 Building REAL250005042545 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042545' /scratch/stefan/7921153/working/building/REAL250005042545 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042545 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042545/0 /scratch/stefan/7921153/working/building/REAL250005042545 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 655) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/655 `/scratch/stefan/7921153/working/3D/655' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042545.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042545.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042545/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042545 none CCCC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 56, 33, 18, 33, 18, 18, 18, 18, 18, 8, 18, 8, 1, 8, 1, 1, 1, 1, 1, 1, 18, 59, 59, 59, 59, 59, 56, 56, 18, 18, 18, 18, 18, 8, 1, 18, 18] 59 rigid atoms, others: [35, 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, 36, 37]) total number of confs: 215 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042545 none CCCC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 24, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 18, 18, 18, 18, 18, 1, 33, 33, 33, 32, 32, 24, 24, 1, 1, 2, 2, 2, 6, 18, 1, 1] 59 rigid atoms, others: [3, 36, 5, 6, 7, 8, 9, 10, 11, 12, 21, 29, 30, 37] set([0, 1, 2, 4, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042545 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042545 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042545/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042545 Building REAL250005042546 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042546' /scratch/stefan/7921153/working/building/REAL250005042546 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042546 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042546/0 /scratch/stefan/7921153/working/building/REAL250005042546 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 656) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/656 `/scratch/stefan/7921153/working/3D/656' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042546.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042546.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042546/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042546 none CC(C)CC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [35, 36, 36, 25, 12, 25, 12, 12, 12, 12, 12, 6, 12, 6, 1, 6, 1, 1, 1, 1, 1, 1, 12, 36, 36, 36, 36, 36, 36, 36, 36, 36, 12, 12, 12, 12, 12, 6, 1, 12, 12] 36 rigid atoms, others: [38, 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, 39, 40]) total number of confs: 139 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042546 none CC(C)CC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [19, 18, 21, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 12, 12, 1, 21, 21, 21, 21, 21, 21, 21, 19, 19, 1, 1, 2, 2, 2, 6, 12, 1, 1] 36 rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 11, 12, 13, 40, 22, 39] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042546 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042546 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042546/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042546 Building REAL250005042547 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042547' /scratch/stefan/7921153/working/building/REAL250005042547 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042547 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042547/0 /scratch/stefan/7921153/working/building/REAL250005042547 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 657) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/657 `/scratch/stefan/7921153/working/3D/657' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC1C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042547.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042547.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042547/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042547 none CC1CC1C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [34, 34, 34, 25, 12, 25, 12, 12, 12, 12, 12, 6, 12, 6, 1, 6, 1, 1, 1, 1, 1, 1, 12, 34, 34, 34, 34, 34, 34, 34, 12, 12, 12, 12, 12, 6, 1, 12, 12] 34 rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 105 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: REAL250005042547 none CC1CC1C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [20, 20, 20, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 12, 12, 1, 20, 20, 20, 20, 20, 20, 20, 1, 1, 2, 2, 2, 6, 12, 1, 1] 34 rigid atoms, others: [4, 37, 6, 7, 8, 9, 10, 11, 12, 13, 22, 38, 30, 31] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36]) total number of confs: 78 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042547 none CC1CC1C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 7, 7, 20, 20, 20, 20, 20, 20, 20, 31, 31, 31, 34, 34, 34, 34, 34, 20, 2, 2, 2, 1, 1, 1, 1, 20, 20, 20, 20, 20, 31, 34, 20, 20] 34 rigid atoms, others: [0, 1, 2, 3, 4, 26, 27, 28, 29] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042547 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042547 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042547/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042547 Building REAL250005042548 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042548' /scratch/stefan/7921153/working/building/REAL250005042548 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042548 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042548/0 /scratch/stefan/7921153/working/building/REAL250005042548 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 658) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/658 `/scratch/stefan/7921153/working/3D/658' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042548.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042548/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042548 none CCOCC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 103, 45, 23, 45, 23, 23, 23, 23, 23, 9, 23, 9, 1, 9, 1, 1, 1, 1, 1, 1, 23, 127, 127, 127, 127, 127, 103, 103, 23, 23, 23, 23, 23, 9, 1, 23, 23] 127 rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 422 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042548 none CCOCC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [77, 69, 32, 7, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 23, 23, 23, 23, 23, 1, 77, 77, 77, 77, 77, 33, 33, 1, 1, 2, 2, 2, 6, 23, 1, 1] 127 rigid atoms, others: [4, 37, 6, 7, 8, 9, 10, 11, 12, 13, 22, 38, 30, 31] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36]) total number of confs: 247 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042548 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042548 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042548/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042548 Building REAL250005042549 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042549' /scratch/stefan/7921153/working/building/REAL250005042549 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042549 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042549/0 /scratch/stefan/7921153/working/building/REAL250005042549 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 659) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/659 `/scratch/stefan/7921153/working/3D/659' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)=CC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042549.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042549/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042549 none CC(C)=CC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 20, 13, 20, 13, 13, 13, 13, 13, 8, 13, 8, 1, 8, 1, 1, 1, 1, 1, 1, 13, 33, 33, 33, 33, 33, 33, 33, 13, 13, 13, 13, 13, 8, 1, 13, 13] 33 rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 103 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042549 none CC(C)=CC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 13, 13, 13, 13, 13, 1, 18, 18, 18, 18, 18, 18, 18, 1, 1, 2, 2, 2, 6, 13, 1, 1] 33 rigid atoms, others: [4, 37, 6, 7, 8, 9, 10, 11, 12, 13, 22, 38, 30, 31] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042549 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042549 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042549/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042549 Building REAL250005042550 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042550' /scratch/stefan/7921153/working/building/REAL250005042550 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042550 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042550/0 /scratch/stefan/7921153/working/building/REAL250005042550 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 660) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/660 `/scratch/stefan/7921153/working/3D/660' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSCC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042550.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042550/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042550 none CSCC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 68, 36, 12, 36, 12, 12, 12, 12, 12, 7, 12, 7, 1, 7, 1, 1, 1, 1, 1, 1, 12, 82, 82, 82, 68, 68, 12, 12, 12, 12, 12, 7, 1, 12, 12] 82 rigid atoms, others: [33, 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, 34, 35]) total number of confs: 273 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042550 none CSCC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [60, 31, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 12, 12, 1, 60, 60, 60, 31, 31, 1, 1, 2, 2, 2, 6, 12, 1, 1] 82 rigid atoms, others: [34, 3, 5, 6, 7, 8, 9, 10, 11, 12, 35, 21, 27, 28] set([0, 1, 2, 4, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042550 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042550 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042550/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042550 Building REAL250005042551 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042551' /scratch/stefan/7921153/working/building/REAL250005042551 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042551 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042551/0 /scratch/stefan/7921153/working/building/REAL250005042551 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 661) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/661 `/scratch/stefan/7921153/working/3D/661' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042551.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042551/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042551 none CCCCC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 107, 96, 38, 18, 38, 18, 18, 18, 18, 18, 8, 18, 8, 1, 8, 1, 1, 1, 1, 1, 1, 18, 114, 114, 114, 114, 114, 108, 108, 96, 96, 18, 18, 18, 18, 18, 8, 1, 18, 18] 114 rigid atoms, others: [38, 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, 39, 40]) total number of confs: 465 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042551 none CCCCC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [68, 43, 33, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 18, 18, 18, 18, 18, 1, 69, 69, 69, 67, 69, 47, 47, 33, 33, 1, 1, 2, 2, 2, 6, 18, 1, 1] 114 rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 11, 12, 13, 40, 22, 39] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38]) total number of confs: 363 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042551 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042551 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042551/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042551 Building REAL250005042552 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042552' /scratch/stefan/7921153/working/building/REAL250005042552 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042552 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042552/0 /scratch/stefan/7921153/working/building/REAL250005042552 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 662) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/662 `/scratch/stefan/7921153/working/3D/662' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042552.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042552/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042552 none CC(C)C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 13, 20, 13, 13, 13, 13, 13, 9, 13, 9, 1, 9, 1, 1, 1, 1, 1, 1, 13, 20, 20, 20, 20, 20, 20, 20, 13, 13, 13, 13, 13, 9, 1, 13, 13] 20 rigid atoms, others: [35, 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, 36, 37]) total number of confs: 51 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042552 none CC(C)C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [9, 5, 9, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 13, 13, 13, 13, 13, 1, 9, 9, 9, 9, 9, 9, 9, 1, 1, 2, 2, 2, 6, 13, 1, 1] 20 rigid atoms, others: [3, 36, 5, 6, 7, 8, 9, 10, 11, 12, 21, 29, 30, 37] set([0, 1, 2, 4, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042552 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042552 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042552/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042552 Building REAL250005042553 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042553' /scratch/stefan/7921153/working/building/REAL250005042553 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042553 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042553/0 /scratch/stefan/7921153/working/building/REAL250005042553 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 663) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/663 `/scratch/stefan/7921153/working/3D/663' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042553.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042553.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042553/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042553 none CCC(C)C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 35, 45, 17, 35, 17, 17, 17, 17, 17, 7, 17, 7, 1, 7, 1, 1, 1, 1, 1, 1, 17, 45, 45, 45, 45, 45, 45, 45, 45, 45, 17, 17, 17, 17, 17, 7, 1, 17, 17] 45 rigid atoms, others: [38, 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, 39, 40]) total number of confs: 151 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042553 none CCC(C)C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [23, 19, 6, 19, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 17, 17, 17, 17, 17, 1, 23, 23, 23, 23, 23, 19, 19, 20, 19, 1, 1, 2, 2, 2, 6, 17, 1, 1] 45 rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 11, 12, 13, 40, 22, 39] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042553 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042553 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042553/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042553 Building REAL250005042554 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042554' /scratch/stefan/7921153/working/building/REAL250005042554 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042554 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042554/0 /scratch/stefan/7921153/working/building/REAL250005042554 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 664) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/664 `/scratch/stefan/7921153/working/3D/664' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C)C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042554.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042554/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042554 none COC(C)C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 26, 40, 11, 26, 11, 11, 11, 11, 11, 6, 11, 6, 1, 6, 1, 1, 1, 1, 1, 1, 11, 40, 40, 40, 40, 40, 40, 40, 11, 11, 11, 11, 11, 7, 1, 11, 11] 40 rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 145 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042554 none COC(C)C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [27, 20, 7, 20, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 11, 11, 11, 11, 11, 1, 27, 27, 27, 20, 20, 20, 20, 1, 1, 2, 2, 2, 6, 11, 1, 1] 40 rigid atoms, others: [4, 37, 6, 7, 8, 9, 10, 11, 12, 13, 22, 38, 30, 31] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36]) total number of confs: 109 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042554 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042554 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042554/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042554 Building REAL250005042555 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042555' /scratch/stefan/7921153/working/building/REAL250005042555 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042555 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042555/0 /scratch/stefan/7921153/working/building/REAL250005042555 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 665) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/665 `/scratch/stefan/7921153/working/3D/665' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCCC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042555.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042555/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042555 none C=CCCC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 100, 42, 19, 42, 19, 19, 19, 19, 19, 9, 19, 9, 1, 9, 1, 1, 1, 1, 1, 1, 19, 113, 113, 113, 113, 113, 100, 100, 19, 19, 19, 19, 19, 9, 1, 19, 19] 113 rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 437 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042555 none C=CCCC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [78, 41, 29, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 19, 19, 19, 19, 19, 1, 78, 78, 78, 41, 41, 29, 29, 1, 1, 2, 2, 2, 6, 19, 1, 1] 113 rigid atoms, others: [4, 37, 6, 7, 8, 9, 10, 11, 12, 13, 22, 38, 30, 31] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36]) total number of confs: 320 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042555 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042555 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042555/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042555 Building REAL250005042556 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042556' /scratch/stefan/7921153/working/building/REAL250005042556 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042556 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042556/0 /scratch/stefan/7921153/working/building/REAL250005042556 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 666) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/666 `/scratch/stefan/7921153/working/3D/666' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C#N)C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042556.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042556/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042556 none CC(C#N)C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.1', 'N.1', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [29, 22, 29, 29, 13, 22, 13, 13, 13, 13, 13, 7, 13, 7, 1, 7, 1, 1, 1, 1, 1, 1, 13, 29, 29, 29, 29, 13, 13, 13, 13, 13, 8, 1, 13, 13] 29 rigid atoms, others: [33, 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, 34, 35]) total number of confs: 107 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042556 none CC(C#N)C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.1', 'N.1', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [16, 6, 16, 16, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 13, 13, 13, 13, 13, 1, 16, 16, 16, 16, 1, 1, 2, 2, 2, 6, 13, 1, 1] 29 rigid atoms, others: [34, 35, 4, 6, 7, 8, 9, 10, 11, 12, 13, 22, 27, 28] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042556 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042556 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042556/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042556 Building REAL250005042557 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042557' /scratch/stefan/7921153/working/building/REAL250005042557 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042557 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042557/0 /scratch/stefan/7921153/working/building/REAL250005042557 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 667) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/667 `/scratch/stefan/7921153/working/3D/667' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=C(C)C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042557.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042557/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042557 none CC=C(C)C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 25, 36, 15, 25, 15, 15, 15, 15, 15, 9, 15, 9, 1, 9, 1, 1, 1, 1, 1, 1, 15, 36, 36, 36, 36, 36, 36, 36, 15, 15, 15, 15, 15, 9, 1, 15, 15] 36 rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 113 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042557 none CC=C(C)C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [18, 18, 7, 18, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 15, 15, 15, 15, 15, 1, 18, 18, 18, 18, 18, 18, 18, 1, 1, 2, 2, 2, 6, 15, 1, 1] 36 rigid atoms, others: [4, 37, 6, 7, 8, 9, 10, 11, 12, 13, 22, 38, 30, 31] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36]) total number of confs: 76 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042557 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042557 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042557/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042557 Building REAL250005042558 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042558' /scratch/stefan/7921153/working/building/REAL250005042558 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042558 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042558/0 /scratch/stefan/7921153/working/building/REAL250005042558 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 668) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/668 `/scratch/stefan/7921153/working/3D/668' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042558.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042558.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042558/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042558 none CCC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [27, 26, 17, 26, 17, 17, 17, 17, 17, 8, 17, 8, 1, 8, 1, 1, 1, 1, 1, 1, 17, 27, 27, 27, 27, 27, 17, 17, 17, 17, 17, 9, 1, 17, 17] 27 rigid atoms, others: [32, 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, 33, 34]) total number of confs: 83 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042558 none CCC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [15, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 17, 17, 17, 17, 17, 1, 16, 16, 16, 15, 15, 1, 1, 2, 2, 2, 6, 17, 1, 1] 27 rigid atoms, others: [33, 2, 4, 5, 6, 7, 8, 9, 10, 11, 34, 20, 26, 27] set([0, 1, 3, 32, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 28, 29, 30, 31]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042558 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042558 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042558/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042558 Building REAL250005042559 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042559' /scratch/stefan/7921153/working/building/REAL250005042559 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042559 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042559/0 /scratch/stefan/7921153/working/building/REAL250005042559 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 669) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/669 `/scratch/stefan/7921153/working/3D/669' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042559.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042559.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042559/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042559 none COCCC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 79, 41, 17, 41, 17, 17, 17, 17, 17, 8, 17, 8, 1, 8, 1, 1, 1, 1, 1, 1, 17, 94, 94, 94, 94, 94, 79, 79, 17, 17, 17, 17, 17, 8, 1, 17, 17] 94 rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 356 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042559 none COCCC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [67, 48, 29, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 17, 17, 17, 17, 17, 1, 67, 67, 67, 48, 48, 29, 29, 1, 1, 2, 2, 2, 6, 17, 1, 1] 94 rigid atoms, others: [4, 37, 6, 7, 8, 9, 10, 11, 12, 13, 22, 38, 30, 31] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36]) total number of confs: 262 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042559 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042559 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042559/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042559 Building REAL250005042560 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042560' /scratch/stefan/7921153/working/building/REAL250005042560 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042560 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042560/0 /scratch/stefan/7921153/working/building/REAL250005042560 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 670) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/670 `/scratch/stefan/7921153/working/3D/670' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042560.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042560.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042560/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042560 none CC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 11, 11, 11, 7, 11, 7, 1, 7, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 7, 1, 11, 11] 11 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31]) total number of confs: 25 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042560 none CC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 11, 11, 11, 11, 11, 1, 5, 4, 4, 1, 1, 2, 2, 2, 6, 11, 1, 1] 11 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 19, 23, 24, 30, 31] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 25, 26, 27, 28, 29]) total number of confs: 37 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042560 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042560 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042560/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042560 Building REAL250005042561 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042561' /scratch/stefan/7921153/working/building/REAL250005042561 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042561 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042561/0 /scratch/stefan/7921153/working/building/REAL250005042561 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 671) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/671 `/scratch/stefan/7921153/working/3D/671' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2CC2)C[C@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005042561.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042561/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042561 none C[C@@H]1CN(C(=O)C2CC2)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 14, 14, 18, 18, 24, 24, 14, 7, 14, 7, 1, 7, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 24, 24, 24, 24, 24, 14, 14, 7, 1] 24 rigid atoms, others: [35, 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]) 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: REAL250005042561 none C[C@@H]1CN(C(=O)C2CC2)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [12, 12, 12, 12, 8, 1, 8, 1, 1, 1, 12, 12, 12, 12, 22, 22, 22, 24, 24, 24, 24, 24, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 12, 12, 22, 24] 24 rigid atoms, others: [5, 7, 8, 9, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 32, 33, 34, 35]) total number of confs: 61 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042561 none C[C@@H]1CN(C(=O)C2CC2)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 4, 4, 12, 12, 1, 1, 1, 1, 6, 6, 6, 14, 14, 14, 14, 14, 2, 2, 2, 1, 1, 12, 12, 12, 12, 12, 1, 1, 6, 14] 24 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 10, 11, 12, 13, 33, 25, 26] set([6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 34, 35]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042561 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042561 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042561/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042561 Building REAL250005042562 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042562' /scratch/stefan/7921153/working/building/REAL250005042562 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042562 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042562/0 /scratch/stefan/7921153/working/building/REAL250005042562 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 672) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/672 `/scratch/stefan/7921153/working/3D/672' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2CCC2)C[C@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005042562.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042562/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042562 none C[C@@H]1CN(C(=O)C2CCC2)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 15, 15, 23, 23, 31, 31, 31, 15, 9, 15, 9, 1, 9, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 31, 31, 31, 31, 31, 31, 31, 15, 15, 9, 1] 31 rigid atoms, others: [38, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 93 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: REAL250005042562 none C[C@@H]1CN(C(=O)C2CCC2)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 7, 1, 7, 1, 1, 1, 1, 17, 17, 17, 17, 28, 28, 28, 31, 31, 31, 31, 31, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1, 1, 17, 17, 28, 31] 31 rigid atoms, others: [32, 33, 34, 5, 7, 8, 9, 10, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 35, 36, 37, 38]) total number of confs: 75 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042562 none C[C@@H]1CN(C(=O)C2CCC2)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 17, 17, 17, 1, 1, 1, 1, 6, 6, 6, 15, 15, 15, 15, 15, 2, 2, 2, 1, 1, 17, 17, 17, 17, 17, 17, 17, 1, 1, 6, 15] 31 rigid atoms, others: [0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 35, 36, 26, 27] set([6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 37, 38]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042562 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042562 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042562/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042562 Building REAL250005042563 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042563' /scratch/stefan/7921153/working/building/REAL250005042563 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042563 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042563/0 /scratch/stefan/7921153/working/building/REAL250005042563 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 673) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/673 `/scratch/stefan/7921153/working/3D/673' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C(N)=O)C[C@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005042563.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042563.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042563/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042563 none C[C@@H]1CN(C(=O)C(N)=O)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 8, 11, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 4, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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: [15, 15, 15, 15, 15, 15, 30, 30, 36, 36, 15, 9, 15, 9, 1, 9, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 36, 36, 15, 15, 9, 1] 36 rigid atoms, others: [32, 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]) total number of confs: 109 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042563 none C[C@@H]1CN(C(=O)C(N)=O)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 8, 11, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 4, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 19, 19, 1, 1, 1, 1, 6, 6, 6, 15, 15, 15, 15, 15, 2, 2, 2, 1, 1, 19, 19, 1, 1, 6, 15] 36 rigid atoms, others: [0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 25, 26, 29, 30] set([32, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 31]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042563 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042563 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042563/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042563 Building REAL250005042564 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042564' /scratch/stefan/7921153/working/building/REAL250005042564 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042564 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042564/0 /scratch/stefan/7921153/working/building/REAL250005042564 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 674) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/674 `/scratch/stefan/7921153/working/3D/674' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C(C)(C)C)C[C@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005042564.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042564.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042564/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042564 none C[C@@H]1CN(C(=O)C(C)(C)C)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 9, 9, 15, 15, 15, 15, 15, 9, 4, 9, 4, 1, 4, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 15, 15, 15, 15, 15, 15, 15, 15, 15, 9, 9, 4, 1] 15 rigid atoms, others: [40, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 47 number of broken/clashed sets: 15 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042564 none C[C@@H]1CN(C(=O)C(C)(C)C)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 1, 1, 1, 1, 6, 6, 6, 9, 9, 9, 9, 9, 2, 2, 2, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 6, 9] 15 rigid atoms, others: [0, 1, 2, 3, 4, 5, 38, 11, 12, 13, 14, 26, 27, 37] set([6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40]) total number of confs: 33 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042564 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042564 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042564/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042564 Building REAL250005042565 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042565' /scratch/stefan/7921153/working/building/REAL250005042565 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042565 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042565/0 /scratch/stefan/7921153/working/building/REAL250005042565 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 675) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/675 `/scratch/stefan/7921153/working/3D/675' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2(C)CC2)C[C@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005042565.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042565/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042565 none C[C@@H]1CN(C(=O)C2(C)CC2)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 11, 14, 14, 20, 20, 20, 11, 7, 11, 7, 1, 7, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 20, 20, 20, 20, 20, 20, 20, 11, 11, 7, 1] 20 rigid atoms, others: [38, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 61 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: REAL250005042565 none C[C@@H]1CN(C(=O)C2(C)CC2)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 3, 1, 3, 1, 1, 1, 1, 9, 9, 9, 9, 17, 17, 17, 20, 20, 20, 20, 20, 9, 9, 9, 9, 9, 2, 2, 2, 1, 1, 1, 1, 9, 9, 17, 20] 20 rigid atoms, others: [32, 33, 34, 5, 7, 8, 9, 10, 31] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38]) total number of confs: 50 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042565 none C[C@@H]1CN(C(=O)C2(C)CC2)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 7, 9, 9, 9, 1, 1, 1, 1, 6, 6, 6, 11, 11, 11, 11, 11, 2, 2, 2, 1, 1, 9, 9, 9, 9, 9, 9, 9, 1, 1, 6, 11] 20 rigid atoms, others: [0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 35, 36, 26, 27] set([6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 37, 38]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042565 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042565 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042565/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042565 Building REAL250005042566 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042566' /scratch/stefan/7921153/working/building/REAL250005042566 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042566 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042566/0 /scratch/stefan/7921153/working/building/REAL250005042566 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 676) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/676 `/scratch/stefan/7921153/working/3D/676' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H]1C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042566.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042566/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042566 none C[C@@H]1C[C@H]1C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 23, 33, 14, 23, 14, 14, 14, 14, 14, 8, 14, 8, 1, 8, 1, 1, 1, 1, 1, 1, 14, 33, 33, 33, 33, 33, 14, 14, 14, 14, 14, 8, 1, 14, 14] 33 rigid atoms, others: [36, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 101 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: REAL250005042566 none C[C@@H]1C[C@H]1C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 7, 19, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 14, 14, 14, 14, 14, 1, 19, 19, 19, 19, 19, 1, 1, 2, 2, 2, 6, 14, 1, 1] 33 rigid atoms, others: [37, 6, 8, 9, 10, 11, 12, 13, 14, 15, 24, 38, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36]) total number of confs: 79 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042566 none C[C@@H]1C[C@H]1C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 8, 8, 19, 19, 19, 19, 19, 19, 19, 30, 30, 30, 33, 33, 33, 33, 33, 19, 2, 2, 2, 1, 1, 19, 19, 19, 19, 19, 30, 33, 19, 19] 33 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042566 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042566 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042566/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042566 Building REAL250005042567 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042567' /scratch/stefan/7921153/working/building/REAL250005042567 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042567 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042567/0 /scratch/stefan/7921153/working/building/REAL250005042567 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 677) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/677 `/scratch/stefan/7921153/working/3D/677' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(F)C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042567.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042567.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042567/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042567 none CCC(F)C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [66, 64, 36, 64, 17, 36, 17, 17, 17, 17, 17, 8, 17, 8, 1, 8, 1, 1, 1, 1, 1, 1, 17, 66, 66, 66, 66, 66, 64, 17, 17, 17, 17, 17, 8, 1, 17, 17] 66 rigid atoms, others: [35, 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, 36, 37]) total number of confs: 246 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042567 none CCC(F)C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [36, 27, 6, 27, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 17, 17, 17, 17, 17, 1, 39, 39, 39, 39, 39, 27, 1, 1, 2, 2, 2, 6, 17, 1, 1] 66 rigid atoms, others: [4, 37, 6, 7, 8, 9, 10, 11, 12, 13, 22, 36, 29, 30] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35]) total number of confs: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042567 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042567 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042567/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042567 Building REAL250005042568 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042568' /scratch/stefan/7921153/working/building/REAL250005042568 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042568 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042568/0 /scratch/stefan/7921153/working/building/REAL250005042568 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 678) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/678 `/scratch/stefan/7921153/working/3D/678' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)CCCF)C[C@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005042568.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042568.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042568/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042568 none C[C@@H]1CN(C(=O)CCCF)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 15, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 106 conformations in input total number of sets (complete confs): 106 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 16, 16, 16, 16, 37, 37, 88, 100, 106, 16, 8, 16, 8, 1, 8, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 88, 88, 106, 106, 106, 106, 16, 16, 8, 1] 106 rigid atoms, others: [37, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 460 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042568 none C[C@@H]1CN(C(=O)CCCF)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 15, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 106 conformations in input total number of sets (complete confs): 106 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 7, 32, 37, 69, 1, 1, 1, 1, 6, 6, 6, 16, 16, 16, 16, 16, 2, 2, 2, 1, 1, 32, 32, 43, 43, 65, 66, 1, 1, 6, 16] 106 rigid atoms, others: [0, 1, 2, 3, 4, 5, 11, 12, 34, 14, 13, 35, 26, 27] set([6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 36, 37]) total number of confs: 345 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042568 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042568 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042568/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042568 Building REAL250005042569 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042569' /scratch/stefan/7921153/working/building/REAL250005042569 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042569 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042569/0 /scratch/stefan/7921153/working/building/REAL250005042569 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 679) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/679 `/scratch/stefan/7921153/working/3D/679' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@@H]1C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042569.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042569.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042569/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042569 none C[C@H]1C[C@@H]1C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [34, 34, 34, 34, 25, 34, 12, 25, 12, 12, 12, 12, 12, 7, 12, 7, 1, 7, 1, 1, 1, 1, 1, 1, 12, 34, 34, 34, 34, 34, 12, 12, 12, 12, 12, 7, 1, 12, 12] 34 rigid atoms, others: [36, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 105 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: REAL250005042569 none C[C@H]1C[C@@H]1C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [20, 20, 20, 20, 6, 20, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 12, 12, 1, 20, 20, 20, 20, 20, 1, 1, 2, 2, 2, 6, 12, 1, 1] 34 rigid atoms, others: [37, 6, 8, 9, 10, 11, 12, 13, 14, 15, 24, 38, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36]) total number of confs: 78 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042569 none C[C@H]1C[C@@H]1C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 7, 7, 20, 20, 20, 20, 20, 20, 20, 31, 31, 31, 34, 34, 34, 34, 34, 20, 2, 2, 2, 1, 1, 20, 20, 20, 20, 20, 31, 34, 20, 20] 34 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042569 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042569 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042569/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042569 Building REAL250005042570 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042570' /scratch/stefan/7921153/working/building/REAL250005042570 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042570 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042570/0 /scratch/stefan/7921153/working/building/REAL250005042570 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 680) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/680 `/scratch/stefan/7921153/working/3D/680' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)CO)C[C@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005042570.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042570.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042570/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042570 none C[C@@H]1CN(C(=O)CO)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [15, 15, 15, 15, 15, 15, 22, 22, 26, 15, 8, 15, 8, 1, 8, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 26, 26, 78, 15, 15, 8, 1] 78 rigid atoms, others: [32, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 165 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042570 none C[C@@H]1CN(C(=O)CO)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 5, 14, 1, 1, 1, 1, 6, 6, 6, 15, 15, 15, 15, 15, 2, 2, 2, 1, 1, 14, 14, 42, 1, 1, 6, 15] 78 rigid atoms, others: [0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 24, 25, 29, 30] set([32, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 31]) total number of confs: 119 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042570 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042570 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042570/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042570 Building REAL250005042571 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042571' /scratch/stefan/7921153/working/building/REAL250005042571 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042571 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042571/0 /scratch/stefan/7921153/working/building/REAL250005042571 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 681) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/681 `/scratch/stefan/7921153/working/3D/681' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2CCO2)C[C@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005042571.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042571/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042571 none C[C@@H]1CN(C(=O)C2CCO2)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [17, 17, 17, 17, 17, 17, 27, 27, 37, 37, 37, 17, 8, 17, 8, 1, 8, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 37, 37, 37, 37, 37, 17, 17, 9, 1] 37 rigid atoms, others: [36, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 115 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: REAL250005042571 none C[C@@H]1CN(C(=O)C2CCO2)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [22, 22, 22, 22, 10, 1, 10, 1, 1, 1, 1, 22, 22, 22, 22, 33, 33, 33, 37, 37, 37, 37, 37, 22, 22, 22, 22, 22, 1, 1, 1, 1, 1, 22, 22, 33, 37] 37 rigid atoms, others: [32, 5, 7, 8, 9, 10, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 33, 34, 35, 36]) total number of confs: 84 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042571 none C[C@@H]1CN(C(=O)C2CCO2)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 22, 22, 22, 1, 1, 1, 1, 6, 6, 6, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 22, 22, 22, 22, 22, 1, 1, 6, 17] 37 rigid atoms, others: [0, 1, 2, 3, 4, 5, 33, 11, 12, 34, 14, 13, 26, 27] set([6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 35, 36]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042571 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042571 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042571/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042571 Building REAL250005042572 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042572' /scratch/stefan/7921153/working/building/REAL250005042572 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042572 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042572/0 /scratch/stefan/7921153/working/building/REAL250005042572 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 682) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/682 `/scratch/stefan/7921153/working/3D/682' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2COC2)C[C@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005042572.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042572.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042572/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042572 none C[C@@H]1CN(C(=O)C2COC2)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 14, 14, 20, 20, 31, 31, 31, 14, 7, 14, 7, 1, 7, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 31, 31, 31, 31, 31, 14, 14, 8, 1] 31 rigid atoms, others: [36, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 97 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: REAL250005042572 none C[C@@H]1CN(C(=O)C2COC2)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [15, 15, 15, 15, 7, 1, 7, 1, 1, 1, 1, 15, 15, 15, 15, 28, 28, 28, 31, 31, 31, 31, 31, 15, 15, 15, 15, 15, 1, 1, 1, 1, 1, 15, 15, 28, 31] 31 rigid atoms, others: [32, 5, 7, 8, 9, 10, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 33, 34, 35, 36]) total number of confs: 76 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042572 none C[C@@H]1CN(C(=O)C2COC2)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 15, 15, 15, 1, 1, 1, 1, 6, 6, 6, 14, 14, 14, 14, 14, 2, 2, 2, 1, 1, 15, 15, 15, 15, 15, 1, 1, 6, 14] 31 rigid atoms, others: [0, 1, 2, 3, 4, 5, 33, 11, 12, 34, 14, 13, 26, 27] set([6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 35, 36]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042572 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042572 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042572/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042572 Building REAL250005042573 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042573' /scratch/stefan/7921153/working/building/REAL250005042573 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042573 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042573/0 /scratch/stefan/7921153/working/building/REAL250005042573 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 683) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/683 `/scratch/stefan/7921153/working/3D/683' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C=CCO)C[C@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005042573.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042573/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042573 none C[C@@H]1CN(C(=O)C=CCO)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 5, 12, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [20, 20, 20, 20, 20, 20, 35, 35, 63, 63, 66, 20, 8, 20, 9, 1, 9, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 63, 63, 66, 66, 198, 20, 20, 9, 1] 198 rigid atoms, others: [36, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 402 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042573 none C[C@@H]1CN(C(=O)C=CCO)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 5, 12, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 198 conformations in input total number of sets (complete confs): 198 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 27, 27, 52, 1, 1, 1, 1, 6, 6, 6, 20, 20, 20, 20, 20, 2, 2, 2, 1, 1, 27, 27, 52, 52, 156, 1, 1, 6, 20] 198 rigid atoms, others: [0, 1, 2, 3, 4, 5, 33, 11, 12, 34, 14, 13, 26, 27] set([6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 35, 36]) total number of confs: 379 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042573 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042573 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042573/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042573 Building REAL250005042574 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042574' /scratch/stefan/7921153/working/building/REAL250005042574 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042574 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042574/0 /scratch/stefan/7921153/working/building/REAL250005042574 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 684) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/684 `/scratch/stefan/7921153/working/3D/684' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC=CC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042574.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042574.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042574/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042574 none CCC=CC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 58, 58, 35, 15, 35, 15, 15, 15, 15, 15, 7, 15, 8, 1, 8, 1, 1, 1, 1, 1, 1, 15, 67, 67, 67, 67, 67, 58, 58, 15, 15, 15, 15, 15, 8, 1, 15, 15] 67 rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 216 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042574 none CCC=CC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [45, 26, 26, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 15, 15, 15, 15, 15, 1, 45, 45, 45, 45, 45, 26, 26, 1, 1, 2, 2, 2, 6, 15, 1, 1] 67 rigid atoms, others: [4, 37, 6, 7, 8, 9, 10, 11, 12, 13, 22, 38, 30, 31] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042574 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042574 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042574/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042574 Building REAL250005042575 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042575' /scratch/stefan/7921153/working/building/REAL250005042575 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042575 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042575/0 /scratch/stefan/7921153/working/building/REAL250005042575 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 685) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/685 `/scratch/stefan/7921153/working/3D/685' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042575.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042575.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042575/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042575 none C#CCCC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 65, 35, 14, 35, 14, 14, 14, 14, 14, 6, 14, 6, 1, 6, 1, 1, 1, 1, 1, 1, 14, 69, 69, 69, 65, 65, 14, 14, 14, 14, 14, 7, 1, 14, 14] 69 rigid atoms, others: [34, 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, 35, 36]) total number of confs: 250 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042575 none C#CCCC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [42, 41, 29, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 14, 14, 14, 14, 14, 1, 42, 41, 41, 29, 29, 1, 1, 2, 2, 2, 6, 14, 1, 1] 69 rigid atoms, others: [35, 4, 6, 7, 8, 9, 10, 11, 12, 13, 22, 36, 28, 29] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042575 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042575 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042575/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042575 Building REAL250005042576 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042576' /scratch/stefan/7921153/working/building/REAL250005042576 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042576 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042576/0 /scratch/stefan/7921153/working/building/REAL250005042576 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 686) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/686 `/scratch/stefan/7921153/working/3D/686' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(O)C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042576.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042576/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042576 none C=CC(O)C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 162 conformations in input total number of sets (complete confs): 162 using faster count positions algorithm for large data unique positions, atoms: [54, 54, 29, 54, 12, 29, 12, 12, 12, 12, 12, 5, 12, 5, 1, 5, 1, 1, 1, 1, 1, 1, 12, 54, 54, 54, 54, 162, 12, 12, 12, 12, 12, 5, 1, 12, 12] 162 rigid atoms, others: [34, 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, 35, 36]) total number of confs: 365 number of broken/clashed sets: 14 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042576 none C=CC(O)C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 162 conformations in input total number of sets (complete confs): 162 using faster count positions algorithm for large data unique positions, atoms: [40, 25, 6, 25, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 12, 12, 1, 40, 40, 40, 25, 75, 1, 1, 2, 2, 2, 6, 12, 1, 1] 162 rigid atoms, others: [35, 4, 6, 7, 8, 9, 10, 11, 12, 13, 22, 36, 28, 29] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34]) total number of confs: 242 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042576 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042576 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042576/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042576 Building REAL250005042577 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042577' /scratch/stefan/7921153/working/building/REAL250005042577 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042577 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042577/0 /scratch/stefan/7921153/working/building/REAL250005042577 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 687) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/687 `/scratch/stefan/7921153/working/3D/687' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042577.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042577/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042577 none CC(O)C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [25, 17, 25, 11, 17, 11, 11, 11, 11, 11, 6, 11, 6, 1, 6, 1, 1, 1, 1, 1, 1, 11, 25, 25, 25, 25, 75, 11, 11, 11, 11, 11, 7, 1, 11, 11] 75 rigid atoms, others: [33, 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, 34, 35]) total number of confs: 166 number of broken/clashed sets: 12 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042577 none CC(O)C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [14, 5, 14, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 11, 11, 11, 11, 11, 1, 14, 14, 14, 14, 42, 1, 1, 2, 2, 2, 6, 11, 1, 1] 75 rigid atoms, others: [34, 3, 5, 6, 7, 8, 9, 10, 11, 12, 35, 21, 27, 28] set([0, 1, 2, 4, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 114 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042577 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042577 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042577/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042577 Building REAL250005042578 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042578' /scratch/stefan/7921153/working/building/REAL250005042578 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042578 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042578/0 /scratch/stefan/7921153/working/building/REAL250005042578 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 688) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/688 `/scratch/stefan/7921153/working/3D/688' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042578.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042578.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042578/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042578 none CC(=O)C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [41, 30, 41, 16, 30, 16, 16, 16, 16, 16, 9, 16, 9, 1, 9, 1, 1, 1, 1, 1, 1, 16, 41, 41, 41, 16, 16, 16, 16, 16, 9, 1, 16, 16] 41 rigid atoms, others: [13, 15, 16, 17, 18, 19, 20, 31] 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, 32, 33]) total number of confs: 125 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042578 none CC(=O)C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [21, 6, 22, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 16, 16, 16, 16, 16, 1, 22, 22, 22, 1, 1, 2, 2, 2, 6, 16, 1, 1] 41 rigid atoms, others: [32, 33, 3, 5, 6, 7, 8, 9, 10, 11, 12, 21, 25, 26] set([0, 1, 2, 4, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 27, 28, 29, 30, 31]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042578 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042578 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042578/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042578 Building REAL250005042579 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042579' /scratch/stefan/7921153/working/building/REAL250005042579 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042579 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042579/0 /scratch/stefan/7921153/working/building/REAL250005042579 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 689) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/689 `/scratch/stefan/7921153/working/3D/689' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2(F)CC2)C[C@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005042579.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042579.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042579/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042579 none C[C@@H]1CN(C(=O)C2(F)CC2)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 15, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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, 11, 11, 11, 20, 20, 31, 31, 31, 11, 7, 11, 7, 1, 7, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 31, 31, 31, 31, 11, 11, 7, 1] 31 rigid atoms, others: [35, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 101 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: REAL250005042579 none C[C@@H]1CN(C(=O)C2(F)CC2)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 15, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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: [18, 18, 18, 18, 8, 1, 8, 1, 1, 1, 1, 18, 18, 18, 18, 29, 29, 29, 31, 31, 31, 31, 31, 18, 18, 18, 18, 18, 1, 1, 1, 1, 18, 18, 29, 31] 31 rigid atoms, others: [5, 7, 8, 9, 10, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35]) total number of confs: 74 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042579 none C[C@@H]1CN(C(=O)C2(F)CC2)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 15, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 18, 18, 18, 1, 1, 1, 1, 6, 6, 6, 11, 11, 11, 11, 11, 2, 2, 2, 1, 1, 18, 18, 18, 18, 1, 1, 6, 11] 31 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 11, 12, 13, 14, 33, 26, 27] set([6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 34, 35]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042579 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042579 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042579/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042579 Building REAL250005042580 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042580' /scratch/stefan/7921153/working/building/REAL250005042580 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042580 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042580/0 /scratch/stefan/7921153/working/building/REAL250005042580 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 690) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/690 `/scratch/stefan/7921153/working/3D/690' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=C(F)C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042580.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042580.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042580/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042580 none CC=C(F)C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 15, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 21, 32, 11, 21, 11, 11, 11, 11, 11, 6, 11, 6, 1, 6, 1, 1, 1, 1, 1, 1, 11, 32, 32, 32, 32, 11, 11, 11, 11, 11, 6, 1, 11, 11] 32 rigid atoms, others: [33, 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, 34, 35]) total number of confs: 95 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042580 none CC=C(F)C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 15, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [24, 23, 6, 24, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 11, 11, 11, 11, 11, 1, 24, 24, 24, 23, 1, 1, 2, 2, 2, 6, 11, 1, 1] 32 rigid atoms, others: [34, 35, 4, 6, 7, 8, 9, 10, 11, 12, 13, 22, 27, 28] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042580 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042580 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042580/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042580 Building REAL250005042581 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042581' /scratch/stefan/7921153/working/building/REAL250005042581 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042581 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042581/0 /scratch/stefan/7921153/working/building/REAL250005042581 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 691) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/691 `/scratch/stefan/7921153/working/3D/691' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CO)C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042581.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042581.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042581/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042581 none CC(CO)C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [28, 20, 28, 29, 10, 20, 10, 10, 10, 10, 10, 3, 10, 3, 1, 3, 1, 1, 1, 1, 1, 1, 10, 28, 28, 28, 28, 29, 29, 87, 10, 10, 10, 10, 10, 4, 1, 10, 10] 87 rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 195 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042581 none CC(CO)C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [14, 5, 14, 21, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 10, 10, 10, 10, 10, 1, 14, 14, 14, 14, 21, 21, 63, 1, 1, 2, 2, 2, 6, 10, 1, 1] 87 rigid atoms, others: [4, 37, 6, 7, 8, 9, 10, 11, 12, 13, 22, 38, 30, 31] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36]) total number of confs: 170 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042581 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042581 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042581/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042581 Building REAL250005042582 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042582' /scratch/stefan/7921153/working/building/REAL250005042582 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042582 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042582/0 /scratch/stefan/7921153/working/building/REAL250005042582 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 692) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/692 `/scratch/stefan/7921153/working/3D/692' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2(O)CC2)C[C@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005042582.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042582.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042582/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042582 none C[C@@H]1CN(C(=O)C2(O)CC2)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [12, 12, 12, 12, 12, 12, 19, 19, 29, 29, 29, 12, 8, 12, 8, 1, 8, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 87, 29, 29, 29, 29, 12, 12, 8, 1] 87 rigid atoms, others: [36, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 178 number of broken/clashed sets: 16 ./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: REAL250005042582 none C[C@@H]1CN(C(=O)C2(O)CC2)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [15, 15, 15, 15, 8, 1, 8, 1, 1, 1, 1, 15, 15, 15, 15, 25, 25, 25, 29, 29, 29, 29, 29, 15, 15, 15, 15, 15, 6, 1, 1, 1, 1, 15, 15, 25, 29] 87 rigid atoms, others: [32, 5, 7, 8, 9, 10, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36]) total number of confs: 76 number of broken/clashed sets: 16 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042582 none C[C@@H]1CN(C(=O)C2(O)CC2)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 87 conformations in input total number of sets (complete confs): 87 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 15, 15, 15, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 12, 12, 2, 2, 2, 1, 1, 45, 15, 15, 15, 15, 1, 1, 6, 12] 87 rigid atoms, others: [0, 1, 2, 3, 4, 5, 33, 11, 12, 34, 14, 13, 26, 27] set([6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 35, 36]) total number of confs: 110 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042582 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042582 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042582/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042582 Building REAL250005042583 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042583' /scratch/stefan/7921153/working/building/REAL250005042583 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042583 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042583/0 /scratch/stefan/7921153/working/building/REAL250005042583 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 693) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/693 `/scratch/stefan/7921153/working/3D/693' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2=CCC2)C[C@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005042583.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042583.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042583/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042583 none C[C@@H]1CN(C(=O)C2=CCC2)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 14, 14, 24, 24, 24, 24, 24, 14, 8, 14, 8, 1, 8, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 24, 24, 24, 24, 24, 14, 14, 8, 1] 24 rigid atoms, others: [36, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 71 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: REAL250005042583 none C[C@@H]1CN(C(=O)C2=CCC2)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 8, 1, 8, 1, 1, 1, 1, 16, 16, 16, 16, 23, 23, 23, 24, 24, 24, 24, 24, 16, 16, 16, 16, 16, 1, 1, 1, 1, 1, 16, 16, 23, 24] 24 rigid atoms, others: [32, 5, 7, 8, 9, 10, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 33, 34, 35, 36]) total number of confs: 55 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042583 none C[C@@H]1CN(C(=O)C2=CCC2)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 7, 16, 16, 16, 1, 1, 1, 1, 6, 6, 6, 14, 14, 14, 14, 14, 2, 2, 2, 1, 1, 16, 16, 16, 16, 16, 1, 1, 6, 14] 24 rigid atoms, others: [0, 1, 2, 3, 4, 5, 33, 11, 12, 34, 14, 13, 26, 27] set([6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 35, 36]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042583 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042583 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042583/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042583 Building REAL250005042584 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042584' /scratch/stefan/7921153/working/building/REAL250005042584 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042584 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042584/0 /scratch/stefan/7921153/working/building/REAL250005042584 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 694) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/694 `/scratch/stefan/7921153/working/3D/694' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CF)C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042584.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042584.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042584/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042584 none CC(CF)C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [29, 21, 29, 31, 10, 21, 10, 10, 10, 10, 10, 5, 10, 5, 1, 5, 1, 1, 1, 1, 1, 1, 10, 29, 29, 29, 29, 31, 31, 10, 10, 10, 10, 10, 6, 1, 10, 10] 31 rigid atoms, others: [35, 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, 36, 37]) total number of confs: 117 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042584 none CC(CF)C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 10, 23, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 10, 10, 10, 10, 10, 1, 10, 10, 10, 10, 23, 23, 1, 1, 2, 2, 2, 6, 10, 1, 1] 31 rigid atoms, others: [4, 37, 6, 7, 8, 9, 10, 11, 12, 13, 22, 36, 29, 30] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042584 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042584 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042584/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042584 Building REAL250005042585 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042585' /scratch/stefan/7921153/working/building/REAL250005042585 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042585 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042585/0 /scratch/stefan/7921153/working/building/REAL250005042585 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 695) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/695 `/scratch/stefan/7921153/working/3D/695' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=CC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042585.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042585.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042585/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042585 none CC=CC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 21, 14, 21, 14, 14, 14, 14, 14, 7, 14, 7, 1, 7, 1, 1, 1, 1, 1, 1, 14, 27, 27, 27, 27, 27, 14, 14, 14, 14, 14, 7, 1, 14, 14] 27 rigid atoms, others: [33, 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, 34, 35]) total number of confs: 79 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042585 none CC=CC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [15, 14, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 14, 14, 14, 14, 14, 1, 15, 15, 15, 14, 15, 1, 1, 2, 2, 2, 6, 14, 1, 1] 27 rigid atoms, others: [34, 3, 5, 6, 7, 8, 9, 10, 11, 12, 35, 21, 27, 28] set([0, 1, 2, 4, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042585 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042585 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042585/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042585 Building REAL250005042586 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042586' /scratch/stefan/7921153/working/building/REAL250005042586 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042586 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042586/0 /scratch/stefan/7921153/working/building/REAL250005042586 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 696) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/696 `/scratch/stefan/7921153/working/3D/696' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C=CCF)C[C@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005042586.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042586.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042586/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042586 none C[C@@H]1CN(C(=O)C=CCF)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'F', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 5, 15, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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: [12, 12, 12, 12, 12, 12, 19, 19, 34, 34, 36, 12, 6, 12, 7, 1, 7, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 34, 34, 36, 36, 12, 12, 7, 1] 36 rigid atoms, others: [35, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 118 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042586 none C[C@@H]1CN(C(=O)C=CCF)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'F', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 5, 15, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 4, 4, 15, 15, 22, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 12, 12, 2, 2, 2, 1, 1, 15, 15, 22, 22, 1, 1, 6, 12] 36 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 11, 12, 13, 14, 33, 26, 27] set([6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 34, 35]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042586 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042586 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042586/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042586 Building REAL250005042587 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042587' /scratch/stefan/7921153/working/building/REAL250005042587 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types Protomer extracton resulted in 0 protomers Marking REAL250005042587 as failed and skipping /scratch/stefan/7921153/working /scratch/stefan/7921153 `/scratch/stefan/7921153/working/building/REAL250005042587' -> `/scratch/stefan/7921153/failed/REAL250005042587' Building REAL250005042588 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042588' /scratch/stefan/7921153/working/building/REAL250005042588 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042588 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042588/0 /scratch/stefan/7921153/working/building/REAL250005042588 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 697) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/697 `/scratch/stefan/7921153/working/3D/697' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](O)C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042588.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042588.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042588/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042588 none C[C@H](O)C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [24, 16, 24, 24, 12, 16, 12, 12, 12, 12, 12, 8, 12, 8, 1, 8, 1, 1, 1, 1, 1, 1, 12, 24, 24, 24, 72, 12, 12, 12, 12, 12, 8, 1, 12, 12] 72 rigid atoms, others: [33, 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, 34, 35]) total number of confs: 155 number of broken/clashed sets: 15 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042588 none C[C@H](O)C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [12, 5, 12, 12, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 12, 12, 1, 12, 12, 12, 36, 1, 1, 2, 2, 2, 6, 12, 1, 1] 72 rigid atoms, others: [34, 35, 4, 6, 7, 8, 9, 10, 11, 12, 13, 22, 27, 28] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 101 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042588 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042588 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042588/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042588 Building REAL250005042589 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042589' /scratch/stefan/7921153/working/building/REAL250005042589 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042589 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042589/0 /scratch/stefan/7921153/working/building/REAL250005042589 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 698) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/698 `/scratch/stefan/7921153/working/3D/698' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CON=CC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042589.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042589.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042589/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042589 none CON=CC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 8, 1, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 34, 14, 34, 14, 14, 14, 14, 14, 7, 14, 7, 1, 7, 1, 1, 1, 1, 1, 1, 14, 56, 56, 56, 56, 14, 14, 14, 14, 14, 7, 1, 14, 14] 56 rigid atoms, others: [33, 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, 34, 35]) total number of confs: 165 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042589 none CON=CC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 8, 1, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [36, 31, 31, 7, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 14, 14, 14, 14, 14, 1, 36, 36, 36, 31, 1, 1, 2, 2, 2, 6, 14, 1, 1] 56 rigid atoms, others: [34, 35, 4, 6, 7, 8, 9, 10, 11, 12, 13, 22, 27, 28] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042589 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042589 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042589/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042589 Building REAL250005042590 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042590' /scratch/stefan/7921153/working/building/REAL250005042590 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042590 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042590/0 /scratch/stefan/7921153/working/building/REAL250005042590 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 699) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/699 `/scratch/stefan/7921153/working/3D/699' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H]1C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042590.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042590.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042590/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042590 none C[C@@H]1C[C@H]1C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 23, 33, 14, 23, 14, 14, 14, 14, 14, 8, 14, 8, 1, 8, 1, 1, 1, 1, 1, 1, 14, 33, 33, 33, 33, 33, 14, 14, 14, 14, 14, 8, 1, 14, 14] 33 rigid atoms, others: [36, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 101 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: REAL250005042590 none C[C@@H]1C[C@H]1C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 7, 19, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 14, 14, 14, 14, 14, 1, 19, 19, 19, 19, 19, 1, 1, 2, 2, 2, 6, 14, 1, 1] 33 rigid atoms, others: [37, 6, 8, 9, 10, 11, 12, 13, 14, 15, 24, 38, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36]) total number of confs: 79 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042590 none C[C@@H]1C[C@H]1C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 8, 8, 19, 19, 19, 19, 19, 19, 19, 30, 30, 30, 33, 33, 33, 33, 33, 19, 2, 2, 2, 1, 1, 19, 19, 19, 19, 19, 30, 33, 19, 19] 33 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042590 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042590 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042590/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042590 Building REAL250005042591 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042591' /scratch/stefan/7921153/working/building/REAL250005042591 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042591 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042591/0 /scratch/stefan/7921153/working/building/REAL250005042591 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 700) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/700 `/scratch/stefan/7921153/working/3D/700' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C(C)(C)O)C[C@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005042591.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042591.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042591/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042591 none C[C@@H]1CN(C(=O)C(C)(C)O)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 11, 11, 11, 11, 21, 21, 26, 26, 26, 11, 5, 11, 5, 1, 5, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 26, 26, 26, 26, 26, 26, 78, 11, 11, 5, 1] 78 rigid atoms, others: [38, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 167 number of broken/clashed sets: 25 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042591 none C[C@@H]1CN(C(=O)C(C)(C)O)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 14, 14, 14, 1, 1, 1, 1, 6, 6, 6, 11, 11, 11, 11, 11, 2, 2, 2, 1, 1, 14, 14, 14, 14, 14, 14, 42, 1, 1, 6, 11] 78 rigid atoms, others: [0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 35, 36, 26, 27] set([6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 37, 38]) total number of confs: 123 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042591 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042591 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042591/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042591 Building REAL250005042592 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042592' /scratch/stefan/7921153/working/building/REAL250005042592 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042592 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042592/0 /scratch/stefan/7921153/working/building/REAL250005042592 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 701) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/701 `/scratch/stefan/7921153/working/3D/701' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C(C)CC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042592.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042592/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042592 none C=C(C)CC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 69, 70, 36, 15, 36, 15, 15, 15, 15, 15, 7, 15, 7, 1, 7, 1, 1, 1, 1, 1, 1, 15, 70, 70, 70, 70, 70, 69, 69, 15, 15, 15, 15, 15, 7, 1, 15, 15] 70 rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 249 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042592 none C=C(C)CC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [45, 30, 45, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 15, 15, 15, 15, 15, 1, 45, 45, 45, 45, 45, 30, 30, 1, 1, 2, 2, 2, 6, 15, 1, 1] 70 rigid atoms, others: [4, 37, 6, 7, 8, 9, 10, 11, 12, 13, 22, 38, 30, 31] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042592 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042592 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042592/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042592 Building REAL250005042593 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042593' /scratch/stefan/7921153/working/building/REAL250005042593 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042593 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042593/0 /scratch/stefan/7921153/working/building/REAL250005042593 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 702) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/702 `/scratch/stefan/7921153/working/3D/702' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042593.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042593.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042593/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042593 none C=CCC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 43, 17, 43, 17, 17, 17, 17, 17, 9, 17, 9, 1, 9, 1, 1, 1, 1, 1, 1, 17, 69, 69, 69, 69, 69, 17, 17, 17, 17, 17, 9, 1, 17, 17] 69 rigid atoms, others: [33, 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, 34, 35]) total number of confs: 239 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042593 none C=CCC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [43, 27, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 17, 17, 17, 17, 17, 1, 43, 43, 43, 27, 27, 1, 1, 2, 2, 2, 6, 17, 1, 1] 69 rigid atoms, others: [34, 3, 5, 6, 7, 8, 9, 10, 11, 12, 35, 21, 27, 28] set([0, 1, 2, 4, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042593 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042593 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042593/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042593 Building REAL250005042594 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042594' /scratch/stefan/7921153/working/building/REAL250005042594 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005042594 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042594/0 /scratch/stefan/7921153/working/building/REAL250005042594 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 703) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/703 `/scratch/stefan/7921153/working/3D/703' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C[NH+](C)C)C[C@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005042594.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042594.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042594/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042594 none C[C@@H]1CN(C(=O)C[NH+](C)C)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 9, 6, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 14, 14, 21, 21, 27, 27, 27, 27, 14, 8, 14, 8, 1, 8, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 27, 27, 27, 27, 27, 27, 27, 27, 14, 14, 8, 1] 27 rigid atoms, others: [40, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 92 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042594 none C[C@@H]1CN(C(=O)C[NH+](C)C)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 9, 6, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 4, 4, 17, 18, 18, 18, 1, 1, 1, 1, 5, 5, 5, 14, 14, 14, 14, 14, 2, 2, 2, 1, 1, 17, 17, 18, 18, 18, 18, 18, 18, 1, 1, 5, 14] 27 rigid atoms, others: [0, 1, 2, 3, 4, 5, 38, 12, 13, 14, 15, 27, 28, 37] set([6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40]) total number of confs: 94 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042594 /scratch/stefan/7921153/working /scratch/stefan/7921153 mkdir: created directory `1' /scratch/stefan/7921153/working/building/REAL250005042594/1 /scratch/stefan/7921153/working/building/REAL250005042594 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 1 (index: 704) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/704 `/scratch/stefan/7921153/working/3D/704' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)CN(C)C)C[C@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005042594.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005042594.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042594/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042594 none C[C@@H]1CN(C(=O)CN(C)C)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 10, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 12, 12, 12, 12, 32, 32, 60, 61, 61, 12, 5, 12, 5, 1, 5, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 60, 60, 61, 61, 61, 61, 61, 61, 12, 12, 5, 1] 61 rigid atoms, others: [39, 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]) total number of confs: 205 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042594 none C[C@@H]1CN(C(=O)CN(C)C)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 10, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 33, 44, 44, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 12, 12, 2, 2, 2, 1, 1, 33, 33, 44, 44, 44, 44, 44, 44, 1, 1, 6, 12] 61 rigid atoms, others: [0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 36, 26, 27, 37] set([6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042594 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042594 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 1: /scratch/stefan/7921153/working/building/REAL250005042594/1.* 0: /scratch/stefan/7921153/working/building/REAL250005042594/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042594 Building REAL250005042595 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042595' /scratch/stefan/7921153/working/building/REAL250005042595 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042595 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042595/0 /scratch/stefan/7921153/working/building/REAL250005042595 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 705) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/705 `/scratch/stefan/7921153/working/3D/705' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)CC#N)C[C@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005042595.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042595.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042595/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042595 none C[C@@H]1CN(C(=O)CC#N)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.1', 'N.1', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 1, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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: [13, 13, 13, 13, 13, 13, 19, 19, 38, 38, 13, 8, 13, 8, 1, 8, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 38, 38, 13, 13, 8, 1] 38 rigid atoms, others: [32, 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]) total number of confs: 137 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042595 none C[C@@H]1CN(C(=O)CC#N)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.1', 'N.1', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 1, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 19, 19, 1, 1, 1, 1, 6, 6, 6, 13, 13, 13, 13, 13, 2, 2, 2, 1, 1, 19, 19, 1, 1, 6, 13] 38 rigid atoms, others: [0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 25, 26, 29, 30] set([32, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 31]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042595 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042595 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042595/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042595 Building REAL250005042596 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042596' /scratch/stefan/7921153/working/building/REAL250005042596 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042596 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042596/0 /scratch/stefan/7921153/working/building/REAL250005042596 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 706) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/706 `/scratch/stefan/7921153/working/3D/706' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2CC2F)C[C@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005042596.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042596/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042596 none C[C@@H]1CN(C(=O)C2CC2F)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 15, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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, 11, 11, 11, 14, 14, 28, 28, 28, 11, 6, 11, 6, 1, 6, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 28, 28, 28, 28, 11, 11, 6, 1] 28 rigid atoms, others: [35, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 81 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042596 none C[C@@H]1CN(C(=O)C2CC2F)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 15, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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: [15, 15, 15, 15, 8, 1, 8, 1, 1, 1, 1, 15, 15, 15, 15, 26, 26, 26, 28, 28, 28, 28, 28, 15, 15, 15, 15, 15, 1, 1, 1, 1, 15, 15, 26, 28] 28 rigid atoms, others: [5, 7, 8, 9, 10, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35]) total number of confs: 72 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042596 none C[C@@H]1CN(C(=O)C2CC2F)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 15, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 4, 4, 15, 15, 15, 1, 1, 1, 1, 6, 6, 6, 11, 11, 11, 11, 11, 2, 2, 2, 1, 1, 15, 15, 15, 15, 1, 1, 6, 11] 28 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 11, 12, 13, 14, 33, 26, 27] set([6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 34, 35]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042596 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042596 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042596/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042596 Building REAL250005042597 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042597' /scratch/stefan/7921153/working/building/REAL250005042597 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042597 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042597/0 /scratch/stefan/7921153/working/building/REAL250005042597 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 707) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/707 `/scratch/stefan/7921153/working/3D/707' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)CCF)C[C@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005042597.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042597/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042597 none C[C@@H]1CN(C(=O)CCF)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 15, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 12, 12, 12, 12, 25, 25, 51, 51, 12, 7, 12, 7, 1, 7, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 51, 51, 51, 51, 12, 12, 7, 1] 51 rigid atoms, others: [34, 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]) total number of confs: 180 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042597 none C[C@@H]1CN(C(=O)CCF)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 15, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 17, 27, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 12, 12, 2, 2, 2, 1, 1, 17, 17, 27, 27, 1, 1, 6, 12] 51 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 10, 11, 12, 13, 25, 26, 31] set([33, 34, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042597 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042597 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042597/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042597 Building REAL250005042598 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042598' /scratch/stefan/7921153/working/building/REAL250005042598 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042598 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042598/0 /scratch/stefan/7921153/working/building/REAL250005042598 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 708) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/708 `/scratch/stefan/7921153/working/3D/708' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H](C)C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042598.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042598.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042598/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042598 none CO[C@H](C)C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [40, 39, 27, 39, 39, 11, 27, 11, 11, 11, 11, 11, 7, 11, 7, 1, 7, 1, 1, 1, 1, 1, 1, 11, 40, 40, 40, 39, 39, 39, 11, 11, 11, 11, 11, 7, 1, 11, 11] 40 rigid atoms, others: [36, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 136 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042598 none CO[C@H](C)C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [24, 18, 7, 18, 18, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 11, 11, 11, 11, 11, 1, 24, 24, 24, 18, 18, 18, 1, 1, 2, 2, 2, 6, 11, 1, 1] 40 rigid atoms, others: [5, 38, 7, 8, 9, 10, 11, 12, 13, 14, 23, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36]) total number of confs: 102 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042598 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042598 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042598/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042598 Building REAL250005042599 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042599' /scratch/stefan/7921153/working/building/REAL250005042599 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042599 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042599/0 /scratch/stefan/7921153/working/building/REAL250005042599 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 709) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/709 `/scratch/stefan/7921153/working/3D/709' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](O)C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042599.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042599.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042599/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042599 none C[C@@H](O)C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [24, 16, 24, 24, 11, 16, 11, 11, 11, 11, 11, 5, 11, 5, 1, 5, 1, 1, 1, 1, 1, 1, 11, 24, 24, 24, 72, 11, 11, 11, 11, 11, 6, 1, 11, 11] 72 rigid atoms, others: [33, 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, 34, 35]) total number of confs: 160 number of broken/clashed sets: 12 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042599 none C[C@@H](O)C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [13, 6, 13, 13, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 11, 11, 11, 11, 11, 1, 13, 13, 13, 39, 1, 1, 2, 2, 2, 6, 11, 1, 1] 72 rigid atoms, others: [34, 35, 4, 6, 7, 8, 9, 10, 11, 12, 13, 22, 27, 28] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 108 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042599 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042599 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042599/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042599 Building REAL250005042600 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042600' /scratch/stefan/7921153/working/building/REAL250005042600 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042600 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042600/0 /scratch/stefan/7921153/working/building/REAL250005042600 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 710) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/710 `/scratch/stefan/7921153/working/3D/710' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C1CC1C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042600.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042600/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042600 none C=C1CC1C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 23, 15, 23, 15, 15, 15, 15, 15, 7, 15, 7, 1, 7, 1, 1, 1, 1, 1, 1, 15, 38, 38, 38, 38, 38, 15, 15, 15, 15, 15, 7, 1, 15, 15] 38 rigid atoms, others: [34, 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, 35, 36]) total number of confs: 117 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: REAL250005042600 none C=C1CC1C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [18, 18, 18, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 15, 15, 15, 15, 15, 1, 18, 18, 18, 18, 18, 1, 1, 2, 2, 2, 6, 15, 1, 1] 38 rigid atoms, others: [35, 4, 6, 7, 8, 9, 10, 11, 12, 13, 22, 36, 28, 29] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34]) total number of confs: 75 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042600 none C=C1CC1C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 8, 8, 18, 18, 18, 18, 18, 18, 18, 34, 34, 34, 38, 38, 38, 38, 38, 18, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18, 34, 38, 18, 18] 38 rigid atoms, others: [0, 1, 2, 3, 4, 23, 24, 25, 26, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042600 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042600 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042600/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042600 Building REAL250005042601 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042601' /scratch/stefan/7921153/working/building/REAL250005042601 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042601 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042601/0 /scratch/stefan/7921153/working/building/REAL250005042601 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 711) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/711 `/scratch/stefan/7921153/working/3D/711' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC1C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042601.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042601.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042601/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042601 none CC1=CC1C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 26, 15, 26, 15, 15, 15, 15, 15, 8, 15, 8, 1, 8, 1, 1, 1, 1, 1, 1, 15, 40, 40, 40, 40, 40, 15, 15, 15, 15, 15, 9, 1, 15, 15] 40 rigid atoms, others: [34, 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, 35, 36]) total number of confs: 119 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: REAL250005042601 none CC1=CC1C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 24, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 15, 15, 15, 15, 15, 1, 24, 24, 24, 24, 24, 1, 1, 2, 2, 2, 6, 15, 1, 1] 40 rigid atoms, others: [35, 4, 6, 7, 8, 9, 10, 11, 12, 13, 22, 36, 28, 29] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34]) total number of confs: 91 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042601 none CC1=CC1C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 9, 9, 24, 24, 24, 24, 24, 24, 24, 37, 37, 37, 40, 40, 40, 40, 40, 24, 2, 2, 2, 1, 1, 24, 24, 24, 24, 24, 37, 40, 24, 24] 40 rigid atoms, others: [0, 1, 2, 3, 4, 26, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042601 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042601 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042601/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042601 Building REAL250005042602 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042602' /scratch/stefan/7921153/working/building/REAL250005042602 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042602 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042602/0 /scratch/stefan/7921153/working/building/REAL250005042602 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 712) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/712 `/scratch/stefan/7921153/working/3D/712' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042602.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042602/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042602 none C=CC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 13, 21, 13, 13, 13, 13, 13, 8, 13, 8, 1, 8, 1, 1, 1, 1, 1, 1, 13, 21, 21, 21, 13, 13, 13, 13, 13, 8, 1, 13, 13] 21 rigid atoms, others: [12, 14, 15, 16, 17, 18, 19, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32]) total number of confs: 57 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042602 none C=CC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 13, 13, 13, 13, 13, 1, 9, 9, 10, 1, 1, 2, 2, 2, 6, 13, 1, 1] 21 rigid atoms, others: [32, 2, 4, 5, 6, 7, 8, 9, 10, 11, 20, 24, 25, 31] set([0, 1, 3, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 26, 27, 28, 29, 30]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042602 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042602 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042602/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042602 Building REAL250005042603 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042603' /scratch/stefan/7921153/working/building/REAL250005042603 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042603 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042603/0 /scratch/stefan/7921153/working/building/REAL250005042603 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 713) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/713 `/scratch/stefan/7921153/working/3D/713' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1OC) `REAL250005042603.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042603/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042603 none CCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [74, 48, 48, 48, 19, 19, 19, 18, 7, 1, 7, 1, 1, 1, 1, 1, 1, 18, 19, 19, 19, 41, 74, 74, 74, 74, 74, 48, 18, 19, 1, 18, 18, 41, 41, 41] 74 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35]) total number of confs: 285 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042603 none CCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [34, 7, 7, 7, 1, 1, 1, 1, 1, 1, 5, 5, 18, 19, 19, 19, 18, 1, 1, 1, 1, 5, 34, 34, 34, 34, 34, 7, 1, 1, 19, 1, 1, 5, 5, 5] 74 rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 28, 29, 31] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 30, 33, 34, 35]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042603 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042603 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042603/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042603 Building REAL250005042604 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042604' /scratch/stefan/7921153/working/building/REAL250005042604 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042604 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042604/0 /scratch/stefan/7921153/working/building/REAL250005042604 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 714) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/714 `/scratch/stefan/7921153/working/3D/714' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(C)=O) `REAL250005042604.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042604/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042604 none CO[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(C)=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 5, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [34, 28, 28, 28, 28, 7, 1, 7, 1, 1, 1, 1, 1, 1, 27, 27, 28, 28, 43, 43, 43, 34, 34, 34, 28, 28, 1, 27, 27, 43, 43, 43, 43] 43 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 26] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32]) total number of confs: 115 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042604 none CO[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(C)=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 5, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 1, 1, 1, 1, 6, 6, 27, 27, 27, 28, 28, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 1, 1, 27, 1, 1, 6, 6, 6, 6] 43 rigid atoms, others: [1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 24, 25, 27, 28] set([0, 32, 7, 8, 9, 10, 11, 12, 13, 18, 19, 20, 21, 22, 23, 26, 29, 30, 31]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042604 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042604 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042604/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042604 Building REAL250005042605 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042605' /scratch/stefan/7921153/working/building/REAL250005042605 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042605 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042605/0 /scratch/stefan/7921153/working/building/REAL250005042605 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 715) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/715 `/scratch/stefan/7921153/working/3D/715' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C1CC1) `REAL250005042605.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042605.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042605/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042605 none CO[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 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: [70, 35, 35, 35, 35, 35, 35, 86, 86, 118, 118, 118, 118, 118, 35, 11, 35, 11, 1, 11, 1, 1, 1, 70, 70, 70, 35, 35, 118, 35, 35, 11, 1, 1, 1, 1, 1] 118 rigid atoms, others: [32, 33, 34, 35, 36, 18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 346 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: REAL250005042605 none CO[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 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: [65, 28, 28, 28, 28, 8, 1, 8, 1, 1, 1, 1, 1, 1, 27, 27, 28, 27, 69, 69, 69, 121, 121, 65, 65, 65, 28, 28, 1, 28, 28, 69, 121, 121, 121, 121, 121] 121 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 28] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 400 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042605 none CO[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 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: [5, 1, 1, 1, 1, 1, 1, 6, 6, 27, 28, 28, 28, 28, 1, 1, 1, 1, 7, 7, 7, 36, 36, 5, 5, 5, 1, 1, 27, 1, 1, 7, 36, 36, 36, 36, 36] 121 rigid atoms, others: [1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 26, 27, 29, 30] set([0, 7, 8, 9, 10, 11, 12, 13, 18, 19, 20, 21, 22, 23, 24, 25, 28, 31, 32, 33, 34, 35, 36]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042605 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042605 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042605/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042605 Building REAL250005042606 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042606' /scratch/stefan/7921153/working/building/REAL250005042606 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042606 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042606/0 /scratch/stefan/7921153/working/building/REAL250005042606 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 716) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/716 `/scratch/stefan/7921153/working/3D/716' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1OC) `REAL250005042606.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042606.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042606/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042606 none COCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 158 conformations in input total number of sets (complete confs): 158 using faster count positions algorithm for large data unique positions, atoms: [158, 148, 73, 73, 73, 30, 29, 29, 29, 9, 1, 9, 1, 1, 1, 1, 1, 1, 29, 29, 29, 30, 63, 158, 158, 158, 150, 150, 73, 29, 29, 1, 29, 29, 63, 63, 63] 158 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36]) total number of confs: 619 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042606 none COCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 158 conformations in input total number of sets (complete confs): 158 using faster count positions algorithm for large data unique positions, atoms: [64, 36, 6, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 29, 29, 29, 29, 29, 1, 1, 1, 1, 5, 64, 64, 64, 38, 38, 6, 1, 1, 29, 1, 1, 5, 5, 5] 158 rigid atoms, others: [32, 33, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 29, 30] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 31, 34, 35, 36]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042606 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042606 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042606/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042606 Building REAL250005042607 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042607' /scratch/stefan/7921153/working/building/REAL250005042607 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042607 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042607/0 /scratch/stefan/7921153/working/building/REAL250005042607 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 717) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/717 `/scratch/stefan/7921153/working/3D/717' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1OC) `REAL250005042607.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042607.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042607/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042607 none CCCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [144, 135, 56, 56, 56, 20, 20, 20, 19, 6, 1, 6, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 47, 146, 146, 146, 146, 146, 135, 135, 56, 20, 19, 1, 20, 20, 47, 47, 47] 146 rigid atoms, others: [33, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38]) total number of confs: 598 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042607 none CCCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [54, 41, 6, 6, 6, 1, 1, 1, 1, 1, 1, 5, 5, 19, 19, 20, 19, 19, 1, 1, 1, 1, 5, 64, 64, 64, 64, 64, 41, 41, 6, 1, 1, 20, 1, 1, 5, 5, 5] 146 rigid atoms, others: [32, 34, 35, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 36, 37, 38]) total number of confs: 361 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042607 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042607 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042607/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042607 Building REAL250005042608 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042608' /scratch/stefan/7921153/working/building/REAL250005042608 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042608 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042608/0 /scratch/stefan/7921153/working/building/REAL250005042608 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 718) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/718 `/scratch/stefan/7921153/working/3D/718' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C(C)C) `REAL250005042608.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042608/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042608 none CO[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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] 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: [66, 30, 30, 30, 30, 9, 1, 9, 1, 1, 1, 1, 1, 1, 29, 30, 30, 30, 70, 70, 70, 103, 103, 66, 66, 66, 30, 30, 1, 29, 29, 70, 103, 103, 103, 103, 103, 103, 103] 103 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 28] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 420 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042608 none CO[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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] 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: [6, 1, 1, 1, 1, 1, 1, 6, 6, 29, 29, 29, 30, 30, 1, 1, 1, 1, 6, 6, 6, 30, 30, 6, 6, 6, 1, 1, 29, 1, 1, 6, 30, 30, 30, 30, 30, 30, 30] 103 rigid atoms, others: [1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 26, 27, 29, 30] set([0, 7, 8, 9, 10, 11, 12, 13, 18, 19, 20, 21, 22, 23, 24, 25, 28, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042608 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042608 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042608/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042608 Building REAL250005042609 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042609' /scratch/stefan/7921153/working/building/REAL250005042609 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042609 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042609/0 /scratch/stefan/7921153/working/building/REAL250005042609 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 719) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/719 `/scratch/stefan/7921153/working/3D/719' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C(N)=O) `REAL250005042609.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042609/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042609 none CO[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [35, 23, 23, 23, 23, 9, 1, 9, 1, 1, 1, 1, 1, 1, 22, 22, 23, 23, 41, 41, 41, 46, 46, 35, 35, 35, 23, 23, 1, 23, 23, 41, 46, 46] 46 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 28] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33]) total number of confs: 145 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042609 none CO[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 4, 6, 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: [5, 1, 1, 1, 1, 1, 1, 7, 7, 22, 23, 23, 23, 23, 1, 1, 1, 1, 6, 6, 6, 14, 14, 5, 5, 5, 1, 1, 22, 1, 1, 6, 14, 14] 46 rigid atoms, others: [1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 26, 27, 29, 30] set([0, 32, 33, 7, 8, 9, 10, 11, 12, 13, 18, 19, 20, 21, 22, 23, 24, 25, 28, 31]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042609 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042609 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042609/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042609 Building REAL250005042610 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042610' /scratch/stefan/7921153/working/building/REAL250005042610 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042610 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042610/0 /scratch/stefan/7921153/working/building/REAL250005042610 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 720) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/720 `/scratch/stefan/7921153/working/3D/720' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1OC) `REAL250005042610.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042610/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042610 none C=CCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1OC NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 174 conformations in input total number of sets (complete confs): 174 using faster count positions algorithm for large data unique positions, atoms: [174, 164, 74, 74, 74, 35, 35, 35, 34, 9, 1, 9, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 78, 174, 174, 174, 164, 164, 74, 34, 34, 1, 35, 35, 78, 78, 78] 174 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36]) total number of confs: 711 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042610 none C=CCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1OC NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 174 conformations in input total number of sets (complete confs): 174 using faster count positions algorithm for large data unique positions, atoms: [78, 36, 5, 5, 5, 1, 1, 1, 1, 1, 1, 6, 6, 34, 34, 34, 34, 34, 1, 1, 1, 1, 5, 78, 78, 78, 36, 36, 5, 1, 1, 34, 1, 1, 5, 5, 5] 174 rigid atoms, others: [32, 33, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 29, 30] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 31, 34, 35, 36]) total number of confs: 293 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042610 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042610 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042610/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042610 Building REAL250005042611 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042611' /scratch/stefan/7921153/working/building/REAL250005042611 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042611 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042611/0 /scratch/stefan/7921153/working/building/REAL250005042611 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 721) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/721 `/scratch/stefan/7921153/working/3D/721' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)CO) `REAL250005042611.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042611/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042611 none CO[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)CO NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 138 conformations in input total number of sets (complete confs): 138 using faster count positions algorithm for large data unique positions, atoms: [40, 24, 24, 24, 24, 8, 1, 8, 1, 1, 1, 1, 1, 1, 23, 23, 24, 23, 42, 42, 42, 46, 40, 40, 40, 24, 24, 1, 24, 24, 42, 46, 46, 138] 138 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 27] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33]) total number of confs: 301 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042611 none CO[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)CO NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 138 conformations in input total number of sets (complete confs): 138 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 6, 6, 23, 24, 24, 24, 24, 1, 1, 1, 1, 6, 6, 6, 18, 5, 5, 5, 1, 1, 23, 1, 1, 6, 19, 19, 57] 138 rigid atoms, others: [1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 25, 26, 28, 29] set([0, 32, 33, 7, 8, 9, 10, 11, 12, 13, 18, 19, 20, 21, 22, 23, 24, 27, 30, 31]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042611 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042611 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042611/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042611 Building REAL250005042612 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042612' /scratch/stefan/7921153/working/building/REAL250005042612 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042612 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042612/0 /scratch/stefan/7921153/working/building/REAL250005042612 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 722) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/722 `/scratch/stefan/7921153/working/3D/722' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C(C)O) `REAL250005042612.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042612/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042612 none CO[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C(C)O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [48, 23, 23, 23, 23, 9, 1, 9, 1, 1, 1, 1, 1, 1, 22, 23, 23, 23, 48, 48, 48, 67, 67, 48, 48, 48, 23, 23, 1, 22, 22, 48, 67, 67, 67, 67, 201] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 28] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 469 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042612 none CO[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C(C)O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 6, 6, 22, 23, 22, 23, 23, 1, 1, 1, 1, 6, 6, 6, 28, 28, 5, 5, 5, 1, 1, 22, 1, 1, 6, 28, 28, 28, 28, 84] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 26, 27, 29, 30] set([0, 7, 8, 9, 10, 11, 12, 13, 18, 19, 20, 21, 22, 23, 24, 25, 28, 31, 32, 33, 34, 35, 36]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042612 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042612 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042612/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042612 Building REAL250005042613 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042613' /scratch/stefan/7921153/working/building/REAL250005042613 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042613 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042613/0 /scratch/stefan/7921153/working/building/REAL250005042613 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 723) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/723 `/scratch/stefan/7921153/working/3D/723' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)[C@@H](C)O) `REAL250005042613.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042613/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042613 none CO[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)[C@@H](C)O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 216 conformations in input total number of sets (complete confs): 216 using faster count positions algorithm for large data unique positions, atoms: [49, 24, 24, 24, 24, 9, 1, 9, 1, 1, 1, 1, 1, 1, 23, 24, 24, 24, 51, 51, 51, 72, 72, 72, 49, 49, 49, 24, 24, 1, 23, 23, 51, 72, 72, 72, 216] 216 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 29] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 501 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042613 none CO[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)[C@@H](C)O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 216 conformations in input total number of sets (complete confs): 216 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 6, 6, 23, 24, 23, 24, 24, 1, 1, 1, 1, 6, 6, 6, 28, 28, 28, 5, 5, 5, 1, 1, 23, 1, 1, 6, 28, 28, 28, 84] 216 rigid atoms, others: [1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 27, 28, 30, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 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/7921153/working/building/REAL250005042613 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042613 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042613/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042613 Building REAL250005042614 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042614' /scratch/stefan/7921153/working/building/REAL250005042614 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042614 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042614/0 /scratch/stefan/7921153/working/building/REAL250005042614 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 724) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/724 `/scratch/stefan/7921153/working/3D/724' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)[C@H](C)O) `REAL250005042614.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042614/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042614 none CO[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)[C@H](C)O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 195 conformations in input total number of sets (complete confs): 195 using faster count positions algorithm for large data unique positions, atoms: [44, 26, 27, 27, 26, 8, 1, 8, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 53, 53, 53, 65, 65, 65, 44, 44, 44, 26, 26, 1, 27, 27, 53, 65, 65, 65, 195] 195 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 29] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 411 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042614 none CO[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)[C@H](C)O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 195 conformations in input total number of sets (complete confs): 195 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 6, 7, 27, 27, 27, 27, 27, 1, 1, 1, 1, 6, 6, 6, 27, 27, 25, 5, 5, 5, 1, 1, 27, 1, 1, 6, 27, 27, 27, 81] 195 rigid atoms, others: [1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 27, 28, 30, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 32, 33, 34, 35, 36]) total number of confs: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042614 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042614 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042614/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042614 Building REAL250005042615 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042615' /scratch/stefan/7921153/working/building/REAL250005042615 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042615 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042615/0 /scratch/stefan/7921153/working/building/REAL250005042615 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 725) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/725 `/scratch/stefan/7921153/working/3D/725' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1OC) `REAL250005042615.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042615/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042615 none CC=CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1OC NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [61, 61, 40, 40, 40, 18, 18, 18, 17, 6, 1, 6, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 35, 61, 61, 61, 61, 61, 40, 17, 17, 1, 18, 18, 35, 35, 35] 61 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36]) total number of confs: 198 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042615 none CC=CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1OC NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 7, 7, 7, 1, 1, 1, 1, 1, 1, 5, 5, 17, 17, 17, 17, 17, 1, 1, 1, 1, 5, 28, 28, 28, 28, 28, 7, 1, 1, 18, 1, 1, 5, 5, 5] 61 rigid atoms, others: [32, 33, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 29, 30] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 31, 34, 35, 36]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042615 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042615 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042615/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042615 Building REAL250005042616 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042616' /scratch/stefan/7921153/working/building/REAL250005042616 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042616 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042616/0 /scratch/stefan/7921153/working/building/REAL250005042616 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 726) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/726 `/scratch/stefan/7921153/working/3D/726' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@H](OC)C1) `REAL250005042616.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042616/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042616 none COCC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@H](OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [81, 68, 31, 13, 31, 13, 13, 5, 13, 5, 1, 5, 1, 1, 1, 1, 1, 1, 13, 13, 13, 23, 13, 81, 81, 81, 68, 68, 13, 13, 5, 1, 23, 23, 23, 13, 13] 81 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36]) total number of confs: 289 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042616 none COCC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@H](OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [50, 22, 6, 1, 6, 1, 1, 1, 1, 1, 6, 6, 6, 13, 13, 13, 13, 13, 1, 1, 1, 5, 1, 50, 50, 50, 22, 22, 1, 1, 6, 13, 5, 5, 5, 1, 1] 81 rigid atoms, others: [35, 3, 36, 5, 6, 7, 8, 9, 18, 19, 20, 22, 28, 29] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 21, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042616 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042616 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042616/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042616 Building REAL250005042617 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042617' /scratch/stefan/7921153/working/building/REAL250005042617 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042617 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042617/0 /scratch/stefan/7921153/working/building/REAL250005042617 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 727) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/727 `/scratch/stefan/7921153/working/3D/727' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@H](OC)C1) `REAL250005042617.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042617/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042617 none CCCC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@H](OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 89 conformations in input total number of sets (complete confs): 89 using faster count positions algorithm for large data unique positions, atoms: [86, 84, 41, 16, 41, 16, 16, 6, 16, 6, 1, 6, 1, 1, 1, 1, 1, 1, 16, 16, 16, 32, 16, 88, 88, 88, 88, 88, 84, 84, 16, 16, 6, 1, 32, 32, 32, 16, 16] 89 rigid atoms, others: [33, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38]) total number of confs: 357 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042617 none CCCC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@H](OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 89 conformations in input total number of sets (complete confs): 89 using faster count positions algorithm for large data unique positions, atoms: [38, 30, 7, 1, 7, 1, 1, 1, 1, 1, 6, 6, 6, 16, 16, 16, 16, 16, 1, 1, 1, 6, 1, 42, 42, 42, 42, 42, 30, 30, 1, 1, 6, 16, 6, 6, 6, 1, 1] 89 rigid atoms, others: [3, 5, 6, 7, 8, 9, 18, 19, 20, 22, 38, 37, 30, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 21, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36]) total number of confs: 227 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042617 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042617 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042617/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042617 Building REAL250005042618 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042618' /scratch/stefan/7921153/working/building/REAL250005042618 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042618 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042618/0 /scratch/stefan/7921153/working/building/REAL250005042618 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 728) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/728 `/scratch/stefan/7921153/working/3D/728' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)C(C)C)C[C@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005042618.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042618.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042618/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042618 none CO[C@@H]1CN(C(=O)C(C)C)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [17, 12, 12, 12, 12, 12, 12, 24, 24, 28, 28, 12, 5, 12, 5, 1, 5, 1, 1, 1, 1, 1, 1, 17, 17, 17, 12, 12, 28, 28, 28, 28, 28, 28, 28, 12, 12, 5, 1] 28 rigid atoms, others: [38, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 99 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042618 none CO[C@@H]1CN(C(=O)C(C)C)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 7, 7, 15, 15, 1, 1, 1, 1, 7, 7, 7, 12, 12, 12, 12, 12, 5, 5, 5, 1, 1, 15, 15, 15, 15, 15, 15, 15, 1, 1, 7, 12] 28 rigid atoms, others: [1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 35, 36, 26, 27] set([0, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 37, 38]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042618 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042618 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042618/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042618 Building REAL250005042619 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042619' /scratch/stefan/7921153/working/building/REAL250005042619 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042619 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042619/0 /scratch/stefan/7921153/working/building/REAL250005042619 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 729) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/729 `/scratch/stefan/7921153/working/3D/729' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@H](OC)C1) `REAL250005042619.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042619.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042619/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042619 none CCC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@H](OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [34, 20, 13, 20, 13, 13, 5, 13, 5, 1, 5, 1, 1, 1, 1, 1, 1, 13, 13, 13, 22, 13, 34, 34, 34, 34, 34, 13, 13, 5, 1, 22, 22, 22, 13, 13] 34 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35]) total number of confs: 142 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042619 none CCC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@H](OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 1, 5, 1, 1, 1, 1, 1, 7, 7, 7, 13, 13, 13, 13, 13, 1, 1, 1, 5, 1, 10, 10, 10, 10, 10, 1, 1, 7, 13, 5, 5, 5, 1, 1] 34 rigid atoms, others: [2, 35, 4, 5, 6, 7, 8, 34, 17, 18, 19, 21, 27, 28] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 20, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042619 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042619 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042619/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042619 Building REAL250005042620 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042620' /scratch/stefan/7921153/working/building/REAL250005042620 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042620 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042620/0 /scratch/stefan/7921153/working/building/REAL250005042620 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 730) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/730 `/scratch/stefan/7921153/working/3D/730' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(C)=O)C[C@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005042620.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042620/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042620 none CO[C@@H]1CN(C(C)=O)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 5, 11, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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: [11, 10, 10, 10, 10, 10, 10, 12, 12, 10, 5, 10, 5, 1, 5, 1, 1, 1, 1, 1, 1, 11, 11, 11, 10, 10, 12, 12, 12, 10, 10, 5, 1] 12 rigid atoms, others: [32, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 35 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042620 none CO[C@@H]1CN(C(C)=O)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 5, 11, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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: [4, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 6, 6, 6, 10, 10, 10, 10, 10, 4, 4, 4, 1, 1, 3, 3, 3, 1, 1, 6, 10] 12 rigid atoms, others: [1, 2, 3, 4, 5, 6, 9, 10, 11, 12, 24, 25, 29, 30] set([0, 32, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 31]) total number of confs: 34 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042620 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042620 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042620/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042620 Building REAL250005042621 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042621' /scratch/stefan/7921153/working/building/REAL250005042621 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042621 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042621/0 /scratch/stefan/7921153/working/building/REAL250005042621 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 731) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/731 `/scratch/stefan/7921153/working/3D/731' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)C2CC2)C[C@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005042621.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042621.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042621/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042621 none CO[C@@H]1CN(C(=O)C2CC2)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [22, 13, 13, 13, 13, 13, 13, 23, 23, 37, 37, 13, 7, 13, 7, 1, 7, 1, 1, 1, 1, 1, 1, 22, 22, 22, 13, 13, 37, 37, 37, 37, 37, 13, 13, 7, 1] 37 rigid atoms, others: [36, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 129 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: REAL250005042621 none CO[C@@H]1CN(C(=O)C2CC2)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [27, 16, 16, 16, 16, 8, 1, 8, 1, 1, 1, 16, 16, 16, 16, 32, 32, 32, 37, 37, 37, 37, 37, 27, 27, 27, 16, 16, 1, 1, 1, 1, 1, 16, 16, 32, 37] 37 rigid atoms, others: [32, 6, 8, 9, 10, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 33, 34, 35, 36]) total number of confs: 106 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042621 none CO[C@@H]1CN(C(=O)C2CC2)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 6, 6, 16, 16, 1, 1, 1, 1, 6, 6, 6, 13, 13, 13, 13, 13, 5, 5, 5, 1, 1, 16, 16, 16, 16, 16, 1, 1, 6, 13] 37 rigid atoms, others: [1, 2, 3, 4, 5, 6, 33, 11, 12, 34, 14, 13, 26, 27] set([0, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 35, 36]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042621 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042621 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042621/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042621 Building REAL250005042622 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042622' /scratch/stefan/7921153/working/building/REAL250005042622 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042622 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042622/0 /scratch/stefan/7921153/working/building/REAL250005042622 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 732) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/732 `/scratch/stefan/7921153/working/3D/732' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)C(N)=O)C[C@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005042622.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042622/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042622 none CO[C@@H]1CN(C(=O)C(N)=O)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 1, 8, 11, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 4, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [14, 9, 9, 9, 9, 9, 9, 15, 15, 26, 26, 9, 4, 9, 4, 1, 4, 1, 1, 1, 1, 1, 1, 14, 14, 14, 9, 9, 26, 26, 9, 9, 4, 1] 26 rigid atoms, others: [33, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 86 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042622 none CO[C@@H]1CN(C(=O)C(N)=O)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 1, 8, 11, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 4, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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: [5, 1, 1, 1, 1, 1, 1, 4, 4, 14, 14, 1, 1, 1, 1, 5, 5, 5, 9, 9, 9, 9, 9, 5, 5, 5, 1, 1, 14, 15, 1, 1, 5, 9] 26 rigid atoms, others: [1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 26, 27, 30, 31] set([0, 32, 33, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042622 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042622 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042622/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042622 Building REAL250005042623 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042623' /scratch/stefan/7921153/working/building/REAL250005042623 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042623 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042623/0 /scratch/stefan/7921153/working/building/REAL250005042623 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 733) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/733 `/scratch/stefan/7921153/working/3D/733' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)CO)C[C@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005042623.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042623/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042623 none CO[C@@H]1CN(C(=O)CO)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [17, 12, 12, 12, 12, 12, 12, 17, 17, 31, 12, 4, 12, 4, 1, 4, 1, 1, 1, 1, 1, 1, 17, 17, 17, 12, 12, 31, 31, 93, 12, 12, 4, 1] 93 rigid atoms, others: [33, 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]) total number of confs: 229 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042623 none CO[C@@H]1CN(C(=O)CO)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 1, 1, 1, 1, 3, 3, 14, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 12, 12, 6, 6, 6, 1, 1, 14, 14, 42, 1, 1, 6, 12] 93 rigid atoms, others: [1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 25, 26, 30, 31] set([0, 32, 33, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29]) total number of confs: 115 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042623 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042623 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042623/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042623 Building REAL250005042624 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042624' /scratch/stefan/7921153/working/building/REAL250005042624 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042624 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042624/0 /scratch/stefan/7921153/working/building/REAL250005042624 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 734) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/734 `/scratch/stefan/7921153/working/3D/734' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)C(C)O)C[C@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005042624.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042624/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042624 none CO[C@@H]1CN(C(=O)C(C)O)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [14, 10, 10, 10, 10, 10, 10, 19, 19, 33, 33, 10, 3, 10, 3, 1, 3, 1, 1, 1, 1, 1, 1, 14, 14, 14, 10, 10, 33, 33, 33, 33, 99, 10, 10, 3, 1] 99 rigid atoms, others: [36, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 232 number of broken/clashed sets: 17 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042624 none CO[C@@H]1CN(C(=O)C(C)O)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 5, 5, 16, 16, 1, 1, 1, 1, 6, 6, 6, 10, 10, 10, 10, 10, 5, 5, 5, 1, 1, 16, 16, 16, 16, 48, 1, 1, 6, 10] 99 rigid atoms, others: [1, 2, 3, 4, 5, 6, 33, 11, 12, 34, 14, 13, 26, 27] set([0, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 35, 36]) total number of confs: 128 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042624 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042624 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042624/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042624 Building REAL250005042625 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042625' /scratch/stefan/7921153/working/building/REAL250005042625 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042625 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042625/0 /scratch/stefan/7921153/working/building/REAL250005042625 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 735) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/735 `/scratch/stefan/7921153/working/3D/735' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)C(C)=O)C[C@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005042625.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042625.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042625/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042625 none CO[C@@H]1CN(C(=O)C(C)=O)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.3', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 1, 5, 11, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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: [12, 8, 8, 8, 8, 8, 8, 14, 14, 24, 24, 8, 3, 8, 3, 1, 3, 1, 1, 1, 1, 1, 1, 12, 12, 12, 8, 8, 24, 24, 24, 8, 8, 3, 1] 24 rigid atoms, others: [34, 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]) total number of confs: 80 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042625 none CO[C@@H]1CN(C(=O)C(C)=O)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.3', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 1, 5, 11, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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: [4, 1, 1, 1, 1, 1, 1, 4, 4, 15, 16, 1, 1, 1, 1, 6, 6, 6, 8, 8, 8, 8, 8, 4, 4, 4, 1, 1, 16, 16, 16, 1, 1, 6, 8] 24 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 26, 27, 31] set([0, 33, 34, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042625 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042625 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042625/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042625 Building REAL250005042626 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042626' /scratch/stefan/7921153/working/building/REAL250005042626 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042626 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042626/0 /scratch/stefan/7921153/working/building/REAL250005042626 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 736) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/736 `/scratch/stefan/7921153/working/3D/736' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=CC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@H](OC)C1) `REAL250005042626.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042626.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042626/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042626 none CC=CC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@H](OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 28, 13, 28, 13, 13, 5, 13, 5, 1, 5, 1, 1, 1, 1, 1, 1, 13, 13, 13, 22, 13, 36, 36, 36, 36, 36, 13, 13, 6, 1, 22, 22, 22, 13, 13] 36 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36]) total number of confs: 120 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042626 none CC=CC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@H](OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [22, 21, 6, 1, 6, 1, 1, 1, 1, 1, 6, 6, 6, 13, 13, 13, 13, 13, 1, 1, 1, 5, 1, 22, 22, 22, 21, 21, 1, 1, 6, 13, 5, 5, 5, 1, 1] 36 rigid atoms, others: [35, 3, 36, 5, 6, 7, 8, 9, 18, 19, 20, 22, 28, 29] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 21, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042626 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042626 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042626/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042626 Building REAL250005042627 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042627' /scratch/stefan/7921153/working/building/REAL250005042627 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042627 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042627/0 /scratch/stefan/7921153/working/building/REAL250005042627 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 737) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/737 `/scratch/stefan/7921153/working/3D/737' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@H](C)O)C[C@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005042627.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042627.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042627/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042627 none CO[C@@H]1CN(C(=O)[C@H](C)O)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [17, 11, 11, 11, 11, 11, 11, 18, 18, 33, 33, 33, 11, 6, 11, 6, 1, 6, 1, 1, 1, 1, 1, 1, 17, 17, 17, 11, 11, 33, 33, 33, 99, 11, 11, 6, 1] 99 rigid atoms, others: [36, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 232 number of broken/clashed sets: 18 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042627 none CO[C@@H]1CN(C(=O)[C@H](C)O)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 5, 5, 15, 15, 15, 1, 1, 1, 1, 6, 6, 6, 11, 11, 11, 11, 11, 5, 5, 5, 1, 1, 15, 15, 15, 45, 1, 1, 6, 11] 99 rigid atoms, others: [1, 2, 3, 4, 5, 6, 33, 12, 13, 14, 15, 34, 27, 28] set([0, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 35, 36]) total number of confs: 120 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042627 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042627 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042627/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042627 Building REAL250005042628 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042628' /scratch/stefan/7921153/working/building/REAL250005042628 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042628 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042628/0 /scratch/stefan/7921153/working/building/REAL250005042628 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 738) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/738 `/scratch/stefan/7921153/working/3D/738' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@H](OC)C1) `REAL250005042628.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042628.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042628/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042628 none C=CCC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@H](OC)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [80, 72, 37, 16, 37, 16, 16, 6, 16, 6, 1, 6, 1, 1, 1, 1, 1, 1, 16, 16, 16, 31, 16, 80, 80, 80, 72, 72, 16, 16, 6, 1, 31, 31, 31, 16, 16] 80 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36]) total number of confs: 313 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042628 none C=CCC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@H](OC)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [52, 30, 7, 1, 7, 1, 1, 1, 1, 1, 6, 6, 6, 16, 16, 16, 16, 16, 1, 1, 1, 5, 1, 52, 52, 52, 30, 30, 1, 1, 6, 16, 5, 5, 5, 1, 1] 80 rigid atoms, others: [35, 3, 36, 5, 6, 7, 8, 9, 18, 19, 20, 22, 28, 29] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 21, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042628 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042628 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042628/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042628 Building REAL250005042629 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042629' /scratch/stefan/7921153/working/building/REAL250005042629 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042629 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042629/0 /scratch/stefan/7921153/working/building/REAL250005042629 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 739) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/739 `/scratch/stefan/7921153/working/3D/739' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)CC#N)C[C@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005042629.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042629.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042629/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042629 none CO[C@@H]1CN(C(=O)CC#N)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.1', 'N.1', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 1, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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: [26, 15, 15, 15, 15, 15, 15, 31, 31, 55, 55, 15, 7, 15, 7, 1, 7, 1, 1, 1, 1, 1, 1, 26, 26, 26, 15, 15, 55, 55, 15, 15, 7, 1] 55 rigid atoms, others: [33, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 218 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042629 none CO[C@@H]1CN(C(=O)CC#N)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.1', 'N.1', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 1, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 6, 6, 26, 26, 1, 1, 1, 1, 6, 6, 6, 15, 15, 15, 15, 15, 5, 5, 5, 1, 1, 26, 26, 1, 1, 6, 15] 55 rigid atoms, others: [1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 26, 27, 30, 31] set([0, 32, 33, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042629 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042629 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042629/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042629 Building REAL250005042630 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042630' /scratch/stefan/7921153/working/building/REAL250005042630 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042630 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042630/0 /scratch/stefan/7921153/working/building/REAL250005042630 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 740) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/740 `/scratch/stefan/7921153/working/3D/740' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@@H](C)O)C[C@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005042630.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042630.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042630/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042630 none CO[C@@H]1CN(C(=O)[C@@H](C)O)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [17, 10, 10, 10, 10, 10, 10, 20, 20, 33, 33, 33, 10, 6, 10, 6, 1, 6, 1, 1, 1, 1, 1, 1, 17, 17, 17, 10, 10, 33, 33, 33, 99, 10, 10, 6, 1] 99 rigid atoms, others: [36, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 232 number of broken/clashed sets: 15 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042630 none CO[C@@H]1CN(C(=O)[C@@H](C)O)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 6, 6, 18, 18, 18, 1, 1, 1, 1, 6, 6, 6, 10, 10, 10, 10, 10, 5, 5, 5, 1, 1, 18, 18, 18, 54, 1, 1, 6, 10] 99 rigid atoms, others: [1, 2, 3, 4, 5, 6, 33, 12, 13, 14, 15, 34, 27, 28] set([0, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 35, 36]) total number of confs: 138 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042630 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042630 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042630/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042630 Building REAL250005042631 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042631' /scratch/stefan/7921153/working/building/REAL250005042631 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042631 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042631/0 /scratch/stefan/7921153/working/building/REAL250005042631 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 741) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/741 `/scratch/stefan/7921153/working/3D/741' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@H](OC)C1) `REAL250005042631.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042631.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042631/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042631 none C=CC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@H](OC)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [23, 20, 10, 20, 10, 10, 4, 10, 4, 1, 4, 1, 1, 1, 1, 1, 1, 10, 10, 10, 15, 10, 23, 23, 23, 10, 10, 4, 1, 15, 15, 15, 10, 10] 23 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33]) total number of confs: 80 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042631 none C=CC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@H](OC)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 1, 4, 1, 1, 1, 1, 1, 6, 6, 6, 10, 10, 10, 10, 10, 1, 1, 1, 5, 1, 9, 10, 10, 1, 1, 6, 10, 5, 5, 5, 1, 1] 23 rigid atoms, others: [32, 33, 2, 4, 5, 6, 7, 8, 17, 18, 19, 21, 25, 26] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 20, 22, 23, 24, 27, 28, 29, 30, 31]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042631 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042631 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042631/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042631 Building REAL250005042632 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042632' /scratch/stefan/7921153/working/building/REAL250005042632 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042632 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042632/0 /scratch/stefan/7921153/working/building/REAL250005042632 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 742) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/742 `/scratch/stefan/7921153/working/3D/742' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042632.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042632/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042632 none CCC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [27, 26, 17, 26, 17, 17, 17, 17, 17, 8, 17, 8, 1, 8, 1, 1, 1, 1, 1, 1, 17, 27, 27, 27, 27, 27, 17, 17, 17, 17, 17, 9, 1, 17, 17] 27 rigid atoms, others: [32, 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, 33, 34]) total number of confs: 83 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042632 none CCC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [15, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 17, 17, 17, 17, 17, 1, 16, 16, 16, 15, 15, 1, 1, 2, 2, 2, 6, 17, 1, 1] 27 rigid atoms, others: [33, 2, 4, 5, 6, 7, 8, 9, 10, 11, 34, 20, 26, 27] set([0, 1, 3, 32, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 28, 29, 30, 31]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042632 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042632 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042632/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042632 Building REAL250005042633 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042633' /scratch/stefan/7921153/working/building/REAL250005042633 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042633 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042633/0 /scratch/stefan/7921153/working/building/REAL250005042633 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 743) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/743 `/scratch/stefan/7921153/working/3D/743' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042633.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042633/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042633 none COCCC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 79, 41, 17, 41, 17, 17, 17, 17, 17, 8, 17, 8, 1, 8, 1, 1, 1, 1, 1, 1, 17, 94, 94, 94, 94, 94, 79, 79, 17, 17, 17, 17, 17, 8, 1, 17, 17] 94 rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 356 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042633 none COCCC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [67, 48, 29, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 17, 17, 17, 17, 17, 1, 67, 67, 67, 48, 48, 29, 29, 1, 1, 2, 2, 2, 6, 17, 1, 1] 94 rigid atoms, others: [4, 37, 6, 7, 8, 9, 10, 11, 12, 13, 22, 38, 30, 31] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36]) total number of confs: 262 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042633 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042633 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042633/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042633 Building REAL250005042634 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042634' /scratch/stefan/7921153/working/building/REAL250005042634 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042634 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042634/0 /scratch/stefan/7921153/working/building/REAL250005042634 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 744) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/744 `/scratch/stefan/7921153/working/3D/744' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042634.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042634/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042634 none CC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 11, 11, 11, 7, 11, 7, 1, 7, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 7, 1, 11, 11] 11 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31]) total number of confs: 25 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042634 none CC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 11, 11, 11, 11, 11, 1, 5, 4, 4, 1, 1, 2, 2, 2, 6, 11, 1, 1] 11 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 19, 23, 24, 30, 31] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 25, 26, 27, 28, 29]) total number of confs: 37 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042634 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042634 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042634/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042634 Building REAL250005042635 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042635' /scratch/stefan/7921153/working/building/REAL250005042635 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042635 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042635/0 /scratch/stefan/7921153/working/building/REAL250005042635 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 745) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/745 `/scratch/stefan/7921153/working/3D/745' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2CC2)C[C@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005042635.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042635.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042635/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042635 none C[C@@H]1CN(C(=O)C2CC2)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 14, 14, 18, 18, 24, 24, 14, 7, 14, 7, 1, 7, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 24, 24, 24, 24, 24, 14, 14, 7, 1] 24 rigid atoms, others: [35, 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]) 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: REAL250005042635 none C[C@@H]1CN(C(=O)C2CC2)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [12, 12, 12, 12, 8, 1, 8, 1, 1, 1, 12, 12, 12, 12, 22, 22, 22, 24, 24, 24, 24, 24, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 12, 12, 22, 24] 24 rigid atoms, others: [5, 7, 8, 9, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 32, 33, 34, 35]) total number of confs: 61 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042635 none C[C@@H]1CN(C(=O)C2CC2)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 4, 4, 12, 12, 1, 1, 1, 1, 6, 6, 6, 14, 14, 14, 14, 14, 2, 2, 2, 1, 1, 12, 12, 12, 12, 12, 1, 1, 6, 14] 24 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 10, 11, 12, 13, 33, 25, 26] set([6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 34, 35]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042635 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042635 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042635/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042635 Building REAL250005042636 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042636' /scratch/stefan/7921153/working/building/REAL250005042636 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042636 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042636/0 /scratch/stefan/7921153/working/building/REAL250005042636 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 746) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/746 `/scratch/stefan/7921153/working/3D/746' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2CCC2)C[C@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005042636.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042636.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042636/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042636 none C[C@@H]1CN(C(=O)C2CCC2)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 15, 15, 23, 23, 31, 31, 31, 15, 9, 15, 9, 1, 9, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 31, 31, 31, 31, 31, 31, 31, 15, 15, 9, 1] 31 rigid atoms, others: [38, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 93 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: REAL250005042636 none C[C@@H]1CN(C(=O)C2CCC2)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 7, 1, 7, 1, 1, 1, 1, 17, 17, 17, 17, 28, 28, 28, 31, 31, 31, 31, 31, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1, 1, 17, 17, 28, 31] 31 rigid atoms, others: [32, 33, 34, 5, 7, 8, 9, 10, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 35, 36, 37, 38]) total number of confs: 75 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042636 none C[C@@H]1CN(C(=O)C2CCC2)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 17, 17, 17, 1, 1, 1, 1, 6, 6, 6, 15, 15, 15, 15, 15, 2, 2, 2, 1, 1, 17, 17, 17, 17, 17, 17, 17, 1, 1, 6, 15] 31 rigid atoms, others: [0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 35, 36, 26, 27] set([6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 37, 38]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042636 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042636 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042636/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042636 Building REAL250005042637 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042637' /scratch/stefan/7921153/working/building/REAL250005042637 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042637 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042637/0 /scratch/stefan/7921153/working/building/REAL250005042637 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 747) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/747 `/scratch/stefan/7921153/working/3D/747' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)CC2CC2)C[C@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005042637.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042637/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042637 none C[C@@H]1CN(C(=O)CC2CC2)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 17, 17, 17, 17, 37, 37, 61, 69, 69, 17, 9, 17, 9, 1, 9, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 61, 61, 69, 69, 69, 69, 69, 17, 17, 9, 1] 69 rigid atoms, others: [38, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 250 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: REAL250005042637 none C[C@@H]1CN(C(=O)CC2CC2)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 35, 35, 14, 3, 14, 1, 1, 1, 1, 35, 35, 35, 35, 65, 65, 65, 69, 69, 69, 69, 69, 35, 35, 35, 35, 35, 3, 3, 1, 1, 1, 1, 1, 35, 35, 65, 69] 69 rigid atoms, others: [32, 33, 34, 7, 8, 9, 10, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38]) total number of confs: 176 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042637 none C[C@@H]1CN(C(=O)CC2CC2)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 27, 35, 35, 1, 1, 1, 1, 6, 6, 6, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 27, 27, 35, 35, 35, 35, 35, 1, 1, 6, 17] 69 rigid atoms, others: [0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 35, 36, 26, 27] set([6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 37, 38]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042637 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042637 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042637/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042637 Building REAL250005042638 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042638' /scratch/stefan/7921153/working/building/REAL250005042638 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042638 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042638/0 /scratch/stefan/7921153/working/building/REAL250005042638 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 748) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/748 `/scratch/stefan/7921153/working/3D/748' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C(C)(C)F)C[C@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005042638.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042638.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042638/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042638 none C[C@@H]1CN(C(=O)C(C)(C)F)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 15, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 10, 17, 17, 21, 21, 21, 10, 6, 10, 6, 1, 6, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 21, 21, 21, 21, 21, 21, 10, 10, 6, 1] 21 rigid atoms, others: [37, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 71 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042638 none C[C@@H]1CN(C(=O)C(C)(C)F)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 15, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 12, 12, 12, 1, 1, 1, 1, 6, 6, 6, 10, 10, 10, 10, 10, 2, 2, 2, 1, 1, 12, 12, 12, 12, 12, 12, 1, 1, 6, 10] 21 rigid atoms, others: [0, 1, 2, 3, 4, 5, 11, 12, 34, 14, 13, 35, 26, 27] set([6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 36, 37]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042638 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042638 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042638/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042638 Building REAL250005042639 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042639' /scratch/stefan/7921153/working/building/REAL250005042639 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042639 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042639/0 /scratch/stefan/7921153/working/building/REAL250005042639 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 749) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/749 `/scratch/stefan/7921153/working/3D/749' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042639.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042639.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042639/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042639 none COCC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 55, 30, 17, 30, 17, 17, 17, 17, 17, 7, 17, 7, 1, 7, 1, 1, 1, 1, 1, 1, 17, 58, 58, 58, 55, 55, 17, 17, 17, 17, 17, 7, 1, 17, 17] 58 rigid atoms, others: [33, 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, 34, 35]) total number of confs: 211 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042639 none COCC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [39, 23, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 17, 17, 17, 17, 17, 1, 40, 40, 40, 23, 23, 1, 1, 2, 2, 2, 6, 17, 1, 1] 58 rigid atoms, others: [34, 3, 5, 6, 7, 8, 9, 10, 11, 12, 35, 21, 27, 28] set([0, 1, 2, 4, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042639 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042639 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042639/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042639 Building REAL250005042640 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042640' /scratch/stefan/7921153/working/building/REAL250005042640 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042640 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042640/0 /scratch/stefan/7921153/working/building/REAL250005042640 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 750) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/750 `/scratch/stefan/7921153/working/3D/750' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042640.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042640.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042640/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042640 none CCCC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 56, 33, 18, 33, 18, 18, 18, 18, 18, 8, 18, 8, 1, 8, 1, 1, 1, 1, 1, 1, 18, 59, 59, 59, 59, 59, 56, 56, 18, 18, 18, 18, 18, 8, 1, 18, 18] 59 rigid atoms, others: [35, 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, 36, 37]) total number of confs: 215 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042640 none CCCC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 24, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 18, 18, 18, 18, 18, 1, 33, 33, 33, 32, 32, 24, 24, 1, 1, 2, 2, 2, 6, 18, 1, 1] 59 rigid atoms, others: [3, 36, 5, 6, 7, 8, 9, 10, 11, 12, 21, 29, 30, 37] set([0, 1, 2, 4, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042640 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042640 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042640/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042640 Building REAL250005042641 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042641' /scratch/stefan/7921153/working/building/REAL250005042641 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042641 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042641/0 /scratch/stefan/7921153/working/building/REAL250005042641 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 751) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/751 `/scratch/stefan/7921153/working/3D/751' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042641.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042641.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042641/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042641 none CC(C)CC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [35, 36, 36, 25, 12, 25, 12, 12, 12, 12, 12, 6, 12, 6, 1, 6, 1, 1, 1, 1, 1, 1, 12, 36, 36, 36, 36, 36, 36, 36, 36, 36, 12, 12, 12, 12, 12, 6, 1, 12, 12] 36 rigid atoms, others: [38, 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, 39, 40]) total number of confs: 139 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042641 none CC(C)CC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [19, 18, 21, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 12, 12, 1, 21, 21, 21, 21, 21, 21, 21, 19, 19, 1, 1, 2, 2, 2, 6, 12, 1, 1] 36 rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 11, 12, 13, 40, 22, 39] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042641 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042641 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042641/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042641 Building REAL250005042642 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042642' /scratch/stefan/7921153/working/building/REAL250005042642 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042642 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042642/0 /scratch/stefan/7921153/working/building/REAL250005042642 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 752) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/752 `/scratch/stefan/7921153/working/3D/752' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC1C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042642.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042642/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042642 none CC1CC1C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [34, 34, 34, 25, 12, 25, 12, 12, 12, 12, 12, 6, 12, 6, 1, 6, 1, 1, 1, 1, 1, 1, 12, 34, 34, 34, 34, 34, 34, 34, 12, 12, 12, 12, 12, 6, 1, 12, 12] 34 rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 105 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: REAL250005042642 none CC1CC1C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [20, 20, 20, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 12, 12, 1, 20, 20, 20, 20, 20, 20, 20, 1, 1, 2, 2, 2, 6, 12, 1, 1] 34 rigid atoms, others: [4, 37, 6, 7, 8, 9, 10, 11, 12, 13, 22, 38, 30, 31] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36]) total number of confs: 78 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042642 none CC1CC1C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 7, 7, 20, 20, 20, 20, 20, 20, 20, 31, 31, 31, 34, 34, 34, 34, 34, 20, 2, 2, 2, 1, 1, 1, 1, 20, 20, 20, 20, 20, 31, 34, 20, 20] 34 rigid atoms, others: [0, 1, 2, 3, 4, 26, 27, 28, 29] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042642 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042642 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042642/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042642 Building REAL250005042643 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042643' /scratch/stefan/7921153/working/building/REAL250005042643 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042643 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042643/0 /scratch/stefan/7921153/working/building/REAL250005042643 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 753) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/753 `/scratch/stefan/7921153/working/3D/753' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042643.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042643.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042643/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042643 none CCOCC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 103, 45, 23, 45, 23, 23, 23, 23, 23, 9, 23, 9, 1, 9, 1, 1, 1, 1, 1, 1, 23, 127, 127, 127, 127, 127, 103, 103, 23, 23, 23, 23, 23, 9, 1, 23, 23] 127 rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 422 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042643 none CCOCC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [77, 69, 32, 7, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 23, 23, 23, 23, 23, 1, 77, 77, 77, 77, 77, 33, 33, 1, 1, 2, 2, 2, 6, 23, 1, 1] 127 rigid atoms, others: [4, 37, 6, 7, 8, 9, 10, 11, 12, 13, 22, 38, 30, 31] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36]) total number of confs: 247 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042643 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042643 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042643/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042643 Building REAL250005042644 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042644' /scratch/stefan/7921153/working/building/REAL250005042644 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042644 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042644/0 /scratch/stefan/7921153/working/building/REAL250005042644 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 754) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/754 `/scratch/stefan/7921153/working/3D/754' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)=CC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042644.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042644/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042644 none CC(C)=CC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 20, 13, 20, 13, 13, 13, 13, 13, 8, 13, 8, 1, 8, 1, 1, 1, 1, 1, 1, 13, 33, 33, 33, 33, 33, 33, 33, 13, 13, 13, 13, 13, 8, 1, 13, 13] 33 rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 103 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042644 none CC(C)=CC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 13, 13, 13, 13, 13, 1, 18, 18, 18, 18, 18, 18, 18, 1, 1, 2, 2, 2, 6, 13, 1, 1] 33 rigid atoms, others: [4, 37, 6, 7, 8, 9, 10, 11, 12, 13, 22, 38, 30, 31] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042644 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042644 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042644/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042644 Building REAL250005042645 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042645' /scratch/stefan/7921153/working/building/REAL250005042645 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042645 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042645/0 /scratch/stefan/7921153/working/building/REAL250005042645 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 755) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/755 `/scratch/stefan/7921153/working/3D/755' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSCC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042645.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042645.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042645/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042645 none CSCC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 68, 36, 12, 36, 12, 12, 12, 12, 12, 7, 12, 7, 1, 7, 1, 1, 1, 1, 1, 1, 12, 82, 82, 82, 68, 68, 12, 12, 12, 12, 12, 7, 1, 12, 12] 82 rigid atoms, others: [33, 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, 34, 35]) total number of confs: 273 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042645 none CSCC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [60, 31, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 12, 12, 1, 60, 60, 60, 31, 31, 1, 1, 2, 2, 2, 6, 12, 1, 1] 82 rigid atoms, others: [34, 3, 5, 6, 7, 8, 9, 10, 11, 12, 35, 21, 27, 28] set([0, 1, 2, 4, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042645 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042645 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042645/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042645 Building REAL250005042646 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042646' /scratch/stefan/7921153/working/building/REAL250005042646 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042646 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042646/0 /scratch/stefan/7921153/working/building/REAL250005042646 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 756) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/756 `/scratch/stefan/7921153/working/3D/756' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042646.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042646/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042646 none CCCCC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 107, 96, 38, 18, 38, 18, 18, 18, 18, 18, 8, 18, 8, 1, 8, 1, 1, 1, 1, 1, 1, 18, 114, 114, 114, 114, 114, 108, 108, 96, 96, 18, 18, 18, 18, 18, 8, 1, 18, 18] 114 rigid atoms, others: [38, 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, 39, 40]) total number of confs: 465 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042646 none CCCCC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [68, 43, 33, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 18, 18, 18, 18, 18, 1, 69, 69, 69, 67, 69, 47, 47, 33, 33, 1, 1, 2, 2, 2, 6, 18, 1, 1] 114 rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 11, 12, 13, 40, 22, 39] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38]) total number of confs: 363 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042646 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042646 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042646/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042646 Building REAL250005042647 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042647' /scratch/stefan/7921153/working/building/REAL250005042647 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042647 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042647/0 /scratch/stefan/7921153/working/building/REAL250005042647 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 757) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/757 `/scratch/stefan/7921153/working/3D/757' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042647.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042647.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042647/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042647 none CC(C)C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 13, 20, 13, 13, 13, 13, 13, 9, 13, 9, 1, 9, 1, 1, 1, 1, 1, 1, 13, 20, 20, 20, 20, 20, 20, 20, 13, 13, 13, 13, 13, 9, 1, 13, 13] 20 rigid atoms, others: [35, 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, 36, 37]) total number of confs: 51 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042647 none CC(C)C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [9, 5, 9, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 13, 13, 13, 13, 13, 1, 9, 9, 9, 9, 9, 9, 9, 1, 1, 2, 2, 2, 6, 13, 1, 1] 20 rigid atoms, others: [3, 36, 5, 6, 7, 8, 9, 10, 11, 12, 21, 29, 30, 37] set([0, 1, 2, 4, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042647 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042647 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042647/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042647 Building REAL250005042648 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042648' /scratch/stefan/7921153/working/building/REAL250005042648 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042648 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042648/0 /scratch/stefan/7921153/working/building/REAL250005042648 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 758) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/758 `/scratch/stefan/7921153/working/3D/758' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042648.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042648.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042648/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042648 none CCC(C)C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 35, 45, 17, 35, 17, 17, 17, 17, 17, 7, 17, 7, 1, 7, 1, 1, 1, 1, 1, 1, 17, 45, 45, 45, 45, 45, 45, 45, 45, 45, 17, 17, 17, 17, 17, 7, 1, 17, 17] 45 rigid atoms, others: [38, 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, 39, 40]) total number of confs: 151 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042648 none CCC(C)C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [23, 19, 6, 19, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 17, 17, 17, 17, 17, 1, 23, 23, 23, 23, 23, 19, 19, 20, 19, 1, 1, 2, 2, 2, 6, 17, 1, 1] 45 rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 11, 12, 13, 40, 22, 39] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042648 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042648 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042648/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042648 Building REAL250005042649 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042649' /scratch/stefan/7921153/working/building/REAL250005042649 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042649 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042649/0 /scratch/stefan/7921153/working/building/REAL250005042649 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 759) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/759 `/scratch/stefan/7921153/working/3D/759' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C)C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042649.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042649.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042649/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042649 none COC(C)C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 26, 40, 11, 26, 11, 11, 11, 11, 11, 6, 11, 6, 1, 6, 1, 1, 1, 1, 1, 1, 11, 40, 40, 40, 40, 40, 40, 40, 11, 11, 11, 11, 11, 7, 1, 11, 11] 40 rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 145 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042649 none COC(C)C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [27, 20, 7, 20, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 11, 11, 11, 11, 11, 1, 27, 27, 27, 20, 20, 20, 20, 1, 1, 2, 2, 2, 6, 11, 1, 1] 40 rigid atoms, others: [4, 37, 6, 7, 8, 9, 10, 11, 12, 13, 22, 38, 30, 31] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36]) total number of confs: 109 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042649 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042649 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042649/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042649 Building REAL250005042650 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042650' /scratch/stefan/7921153/working/building/REAL250005042650 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042650 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042650/0 /scratch/stefan/7921153/working/building/REAL250005042650 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 760) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/760 `/scratch/stefan/7921153/working/3D/760' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCCC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042650.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042650.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042650/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042650 none C=CCCC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 100, 42, 19, 42, 19, 19, 19, 19, 19, 9, 19, 9, 1, 9, 1, 1, 1, 1, 1, 1, 19, 113, 113, 113, 113, 113, 100, 100, 19, 19, 19, 19, 19, 9, 1, 19, 19] 113 rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 437 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042650 none C=CCCC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [78, 41, 29, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 19, 19, 19, 19, 19, 1, 78, 78, 78, 41, 41, 29, 29, 1, 1, 2, 2, 2, 6, 19, 1, 1] 113 rigid atoms, others: [4, 37, 6, 7, 8, 9, 10, 11, 12, 13, 22, 38, 30, 31] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36]) total number of confs: 320 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042650 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042650 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042650/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042650 Building REAL250005042651 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042651' /scratch/stefan/7921153/working/building/REAL250005042651 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042651 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042651/0 /scratch/stefan/7921153/working/building/REAL250005042651 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 761) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/761 `/scratch/stefan/7921153/working/3D/761' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=C(C)C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042651.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042651.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042651/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042651 none CC=C(C)C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 25, 36, 15, 25, 15, 15, 15, 15, 15, 9, 15, 9, 1, 9, 1, 1, 1, 1, 1, 1, 15, 36, 36, 36, 36, 36, 36, 36, 15, 15, 15, 15, 15, 9, 1, 15, 15] 36 rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 113 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042651 none CC=C(C)C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [18, 18, 7, 18, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 15, 15, 15, 15, 15, 1, 18, 18, 18, 18, 18, 18, 18, 1, 1, 2, 2, 2, 6, 15, 1, 1] 36 rigid atoms, others: [4, 37, 6, 7, 8, 9, 10, 11, 12, 13, 22, 38, 30, 31] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36]) total number of confs: 76 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042651 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042651 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042651/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042651 Building REAL250005042652 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042652' /scratch/stefan/7921153/working/building/REAL250005042652 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042652 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042652/0 /scratch/stefan/7921153/working/building/REAL250005042652 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 762) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/762 `/scratch/stefan/7921153/working/3D/762' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2(C)CC2)C[C@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005042652.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042652/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042652 none C[C@@H]1CN(C(=O)C2(C)CC2)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 11, 14, 14, 20, 20, 20, 11, 7, 11, 7, 1, 7, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 20, 20, 20, 20, 20, 20, 20, 11, 11, 7, 1] 20 rigid atoms, others: [38, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 61 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: REAL250005042652 none C[C@@H]1CN(C(=O)C2(C)CC2)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 3, 1, 3, 1, 1, 1, 1, 9, 9, 9, 9, 17, 17, 17, 20, 20, 20, 20, 20, 9, 9, 9, 9, 9, 2, 2, 2, 1, 1, 1, 1, 9, 9, 17, 20] 20 rigid atoms, others: [32, 33, 34, 5, 7, 8, 9, 10, 31] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38]) total number of confs: 50 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042652 none C[C@@H]1CN(C(=O)C2(C)CC2)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 7, 9, 9, 9, 1, 1, 1, 1, 6, 6, 6, 11, 11, 11, 11, 11, 2, 2, 2, 1, 1, 9, 9, 9, 9, 9, 9, 9, 1, 1, 6, 11] 20 rigid atoms, others: [0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 35, 36, 26, 27] set([6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 37, 38]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042652 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042652 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042652/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042652 Building REAL250005042653 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042653' /scratch/stefan/7921153/working/building/REAL250005042653 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042653 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042653/0 /scratch/stefan/7921153/working/building/REAL250005042653 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 763) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/763 `/scratch/stefan/7921153/working/3D/763' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H]1C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042653.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042653/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042653 none C[C@@H]1C[C@H]1C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 23, 33, 14, 23, 14, 14, 14, 14, 14, 8, 14, 8, 1, 8, 1, 1, 1, 1, 1, 1, 14, 33, 33, 33, 33, 33, 14, 14, 14, 14, 14, 8, 1, 14, 14] 33 rigid atoms, others: [36, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 101 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: REAL250005042653 none C[C@@H]1C[C@H]1C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 7, 19, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 14, 14, 14, 14, 14, 1, 19, 19, 19, 19, 19, 1, 1, 2, 2, 2, 6, 14, 1, 1] 33 rigid atoms, others: [37, 6, 8, 9, 10, 11, 12, 13, 14, 15, 24, 38, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36]) total number of confs: 79 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042653 none C[C@@H]1C[C@H]1C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 8, 8, 19, 19, 19, 19, 19, 19, 19, 30, 30, 30, 33, 33, 33, 33, 33, 19, 2, 2, 2, 1, 1, 19, 19, 19, 19, 19, 30, 33, 19, 19] 33 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042653 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042653 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042653/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042653 Building REAL250005042654 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042654' /scratch/stefan/7921153/working/building/REAL250005042654 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042654 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042654/0 /scratch/stefan/7921153/working/building/REAL250005042654 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 764) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/764 `/scratch/stefan/7921153/working/3D/764' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(F)C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042654.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042654/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042654 none CCC(F)C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [66, 64, 36, 64, 17, 36, 17, 17, 17, 17, 17, 8, 17, 8, 1, 8, 1, 1, 1, 1, 1, 1, 17, 66, 66, 66, 66, 66, 64, 17, 17, 17, 17, 17, 8, 1, 17, 17] 66 rigid atoms, others: [35, 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, 36, 37]) total number of confs: 246 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042654 none CCC(F)C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [36, 27, 6, 27, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 17, 17, 17, 17, 17, 1, 39, 39, 39, 39, 39, 27, 1, 1, 2, 2, 2, 6, 17, 1, 1] 66 rigid atoms, others: [4, 37, 6, 7, 8, 9, 10, 11, 12, 13, 22, 36, 29, 30] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35]) total number of confs: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042654 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042654 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042654/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042654 Building REAL250005042655 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042655' /scratch/stefan/7921153/working/building/REAL250005042655 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042655 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042655/0 /scratch/stefan/7921153/working/building/REAL250005042655 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 765) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/765 `/scratch/stefan/7921153/working/3D/765' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)CCCF)C[C@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005042655.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042655/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042655 none C[C@@H]1CN(C(=O)CCCF)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 15, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 106 conformations in input total number of sets (complete confs): 106 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 16, 16, 16, 16, 37, 37, 88, 100, 106, 16, 8, 16, 8, 1, 8, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 88, 88, 106, 106, 106, 106, 16, 16, 8, 1] 106 rigid atoms, others: [37, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 460 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042655 none C[C@@H]1CN(C(=O)CCCF)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 15, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 106 conformations in input total number of sets (complete confs): 106 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 7, 32, 37, 69, 1, 1, 1, 1, 6, 6, 6, 16, 16, 16, 16, 16, 2, 2, 2, 1, 1, 32, 32, 43, 43, 65, 66, 1, 1, 6, 16] 106 rigid atoms, others: [0, 1, 2, 3, 4, 5, 11, 12, 34, 14, 13, 35, 26, 27] set([6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 36, 37]) total number of confs: 345 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042655 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042655 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042655/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042655 Building REAL250005042656 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042656' /scratch/stefan/7921153/working/building/REAL250005042656 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042656 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042656/0 /scratch/stefan/7921153/working/building/REAL250005042656 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 766) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/766 `/scratch/stefan/7921153/working/3D/766' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@@H]1C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042656.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042656/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042656 none C[C@H]1C[C@@H]1C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [34, 34, 34, 34, 25, 34, 12, 25, 12, 12, 12, 12, 12, 7, 12, 7, 1, 7, 1, 1, 1, 1, 1, 1, 12, 34, 34, 34, 34, 34, 12, 12, 12, 12, 12, 7, 1, 12, 12] 34 rigid atoms, others: [36, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 105 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: REAL250005042656 none C[C@H]1C[C@@H]1C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [20, 20, 20, 20, 6, 20, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 12, 12, 1, 20, 20, 20, 20, 20, 1, 1, 2, 2, 2, 6, 12, 1, 1] 34 rigid atoms, others: [37, 6, 8, 9, 10, 11, 12, 13, 14, 15, 24, 38, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36]) total number of confs: 78 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042656 none C[C@H]1C[C@@H]1C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 7, 7, 20, 20, 20, 20, 20, 20, 20, 31, 31, 31, 34, 34, 34, 34, 34, 20, 2, 2, 2, 1, 1, 20, 20, 20, 20, 20, 31, 34, 20, 20] 34 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042656 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042656 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042656/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042656 Building REAL250005042657 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042657' /scratch/stefan/7921153/working/building/REAL250005042657 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042657 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042657/0 /scratch/stefan/7921153/working/building/REAL250005042657 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 767) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/767 `/scratch/stefan/7921153/working/3D/767' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C(N)=O)C[C@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005042657.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042657.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042657/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042657 none C[C@@H]1CN(C(=O)C(N)=O)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 8, 11, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 4, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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: [15, 15, 15, 15, 15, 15, 30, 30, 36, 36, 15, 9, 15, 9, 1, 9, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 36, 36, 15, 15, 9, 1] 36 rigid atoms, others: [32, 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]) total number of confs: 109 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042657 none C[C@@H]1CN(C(=O)C(N)=O)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 8, 11, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 4, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 19, 19, 1, 1, 1, 1, 6, 6, 6, 15, 15, 15, 15, 15, 2, 2, 2, 1, 1, 19, 19, 1, 1, 6, 15] 36 rigid atoms, others: [0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 25, 26, 29, 30] set([32, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 31]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042657 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042657 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042657/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042657 Building REAL250005042658 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042658' /scratch/stefan/7921153/working/building/REAL250005042658 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042658 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042658/0 /scratch/stefan/7921153/working/building/REAL250005042658 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 768) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/768 `/scratch/stefan/7921153/working/3D/768' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C(C)(C)C)C[C@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005042658.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042658/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042658 none C[C@@H]1CN(C(=O)C(C)(C)C)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 9, 9, 15, 15, 15, 15, 15, 9, 4, 9, 4, 1, 4, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 15, 15, 15, 15, 15, 15, 15, 15, 15, 9, 9, 4, 1] 15 rigid atoms, others: [40, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 47 number of broken/clashed sets: 15 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042658 none C[C@@H]1CN(C(=O)C(C)(C)C)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 1, 1, 1, 1, 6, 6, 6, 9, 9, 9, 9, 9, 2, 2, 2, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 6, 9] 15 rigid atoms, others: [0, 1, 2, 3, 4, 5, 38, 11, 12, 13, 14, 26, 27, 37] set([6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40]) total number of confs: 33 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042658 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042658 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042658/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042658 Building REAL250005042659 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042659' /scratch/stefan/7921153/working/building/REAL250005042659 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042659 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042659/0 /scratch/stefan/7921153/working/building/REAL250005042659 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 769) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/769 `/scratch/stefan/7921153/working/3D/769' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042659.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042659.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042659/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042659 none C=CCC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 43, 17, 43, 17, 17, 17, 17, 17, 9, 17, 9, 1, 9, 1, 1, 1, 1, 1, 1, 17, 69, 69, 69, 69, 69, 17, 17, 17, 17, 17, 9, 1, 17, 17] 69 rigid atoms, others: [33, 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, 34, 35]) total number of confs: 239 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042659 none C=CCC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [43, 27, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 17, 17, 17, 17, 17, 1, 43, 43, 43, 27, 27, 1, 1, 2, 2, 2, 6, 17, 1, 1] 69 rigid atoms, others: [34, 3, 5, 6, 7, 8, 9, 10, 11, 12, 35, 21, 27, 28] set([0, 1, 2, 4, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042659 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042659 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042659/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042659 Building REAL250005042660 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042660' /scratch/stefan/7921153/working/building/REAL250005042660 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005042660 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042660/0 /scratch/stefan/7921153/working/building/REAL250005042660 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 770) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/770 `/scratch/stefan/7921153/working/3D/770' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C[NH+](C)C)C[C@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005042660.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042660.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042660/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042660 none C[C@@H]1CN(C(=O)C[NH+](C)C)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 9, 6, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 14, 14, 21, 21, 27, 27, 27, 27, 14, 8, 14, 8, 1, 8, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 27, 27, 27, 27, 27, 27, 27, 27, 14, 14, 8, 1] 27 rigid atoms, others: [40, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 92 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042660 none C[C@@H]1CN(C(=O)C[NH+](C)C)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 9, 6, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 4, 4, 17, 18, 18, 18, 1, 1, 1, 1, 5, 5, 5, 14, 14, 14, 14, 14, 2, 2, 2, 1, 1, 17, 17, 18, 18, 18, 18, 18, 18, 1, 1, 5, 14] 27 rigid atoms, others: [0, 1, 2, 3, 4, 5, 38, 12, 13, 14, 15, 27, 28, 37] set([6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40]) total number of confs: 94 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042660 /scratch/stefan/7921153/working /scratch/stefan/7921153 mkdir: created directory `1' /scratch/stefan/7921153/working/building/REAL250005042660/1 /scratch/stefan/7921153/working/building/REAL250005042660 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 1 (index: 771) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/771 `/scratch/stefan/7921153/working/3D/771' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)CN(C)C)C[C@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005042660.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005042660.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042660/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042660 none C[C@@H]1CN(C(=O)CN(C)C)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 10, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 12, 12, 12, 12, 32, 32, 60, 61, 61, 12, 5, 12, 5, 1, 5, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 60, 60, 61, 61, 61, 61, 61, 61, 12, 12, 5, 1] 61 rigid atoms, others: [39, 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]) total number of confs: 205 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042660 none C[C@@H]1CN(C(=O)CN(C)C)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 10, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 33, 44, 44, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 12, 12, 2, 2, 2, 1, 1, 33, 33, 44, 44, 44, 44, 44, 44, 1, 1, 6, 12] 61 rigid atoms, others: [0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 36, 26, 27, 37] set([6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042660 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042660 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 1: /scratch/stefan/7921153/working/building/REAL250005042660/1.* 0: /scratch/stefan/7921153/working/building/REAL250005042660/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042660 Building REAL250005042661 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042661' /scratch/stefan/7921153/working/building/REAL250005042661 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042661 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042661/0 /scratch/stefan/7921153/working/building/REAL250005042661 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 772) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/772 `/scratch/stefan/7921153/working/3D/772' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(O)C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042661.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042661/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042661 none C=CC(O)C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 162 conformations in input total number of sets (complete confs): 162 using faster count positions algorithm for large data unique positions, atoms: [54, 54, 29, 54, 12, 29, 12, 12, 12, 12, 12, 5, 12, 5, 1, 5, 1, 1, 1, 1, 1, 1, 12, 54, 54, 54, 54, 162, 12, 12, 12, 12, 12, 5, 1, 12, 12] 162 rigid atoms, others: [34, 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, 35, 36]) total number of confs: 365 number of broken/clashed sets: 14 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042661 none C=CC(O)C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 162 conformations in input total number of sets (complete confs): 162 using faster count positions algorithm for large data unique positions, atoms: [40, 25, 6, 25, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 12, 12, 1, 40, 40, 40, 25, 75, 1, 1, 2, 2, 2, 6, 12, 1, 1] 162 rigid atoms, others: [35, 4, 6, 7, 8, 9, 10, 11, 12, 13, 22, 36, 28, 29] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34]) total number of confs: 242 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042661 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042661 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042661/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042661 Building REAL250005042662 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042662' /scratch/stefan/7921153/working/building/REAL250005042662 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042662 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042662/0 /scratch/stefan/7921153/working/building/REAL250005042662 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 773) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/773 `/scratch/stefan/7921153/working/3D/773' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2COC2)C[C@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005042662.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042662.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042662/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042662 none C[C@@H]1CN(C(=O)C2COC2)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 14, 14, 20, 20, 31, 31, 31, 14, 7, 14, 7, 1, 7, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 31, 31, 31, 31, 31, 14, 14, 8, 1] 31 rigid atoms, others: [36, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 97 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: REAL250005042662 none C[C@@H]1CN(C(=O)C2COC2)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [15, 15, 15, 15, 7, 1, 7, 1, 1, 1, 1, 15, 15, 15, 15, 28, 28, 28, 31, 31, 31, 31, 31, 15, 15, 15, 15, 15, 1, 1, 1, 1, 1, 15, 15, 28, 31] 31 rigid atoms, others: [32, 5, 7, 8, 9, 10, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 33, 34, 35, 36]) total number of confs: 76 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042662 none C[C@@H]1CN(C(=O)C2COC2)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 15, 15, 15, 1, 1, 1, 1, 6, 6, 6, 14, 14, 14, 14, 14, 2, 2, 2, 1, 1, 15, 15, 15, 15, 15, 1, 1, 6, 14] 31 rigid atoms, others: [0, 1, 2, 3, 4, 5, 33, 11, 12, 34, 14, 13, 26, 27] set([6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 35, 36]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042662 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042662 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042662/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042662 Building REAL250005042663 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042663' /scratch/stefan/7921153/working/building/REAL250005042663 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042663 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042663/0 /scratch/stefan/7921153/working/building/REAL250005042663 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 774) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/774 `/scratch/stefan/7921153/working/3D/774' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H](C)C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042663.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042663/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042663 none CO[C@H](C)C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [40, 39, 27, 39, 39, 11, 27, 11, 11, 11, 11, 11, 7, 11, 7, 1, 7, 1, 1, 1, 1, 1, 1, 11, 40, 40, 40, 39, 39, 39, 11, 11, 11, 11, 11, 7, 1, 11, 11] 40 rigid atoms, others: [36, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 136 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042663 none CO[C@H](C)C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [24, 18, 7, 18, 18, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 11, 11, 11, 11, 11, 1, 24, 24, 24, 18, 18, 18, 1, 1, 2, 2, 2, 6, 11, 1, 1] 40 rigid atoms, others: [5, 38, 7, 8, 9, 10, 11, 12, 13, 14, 23, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36]) total number of confs: 102 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042663 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042663 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042663/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042663 Building REAL250005042664 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042664' /scratch/stefan/7921153/working/building/REAL250005042664 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042664 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042664/0 /scratch/stefan/7921153/working/building/REAL250005042664 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 775) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/775 `/scratch/stefan/7921153/working/3D/775' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC=CC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042664.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042664/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042664 none CCC=CC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 58, 58, 35, 15, 35, 15, 15, 15, 15, 15, 7, 15, 8, 1, 8, 1, 1, 1, 1, 1, 1, 15, 67, 67, 67, 67, 67, 58, 58, 15, 15, 15, 15, 15, 8, 1, 15, 15] 67 rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 216 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042664 none CCC=CC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [45, 26, 26, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 15, 15, 15, 15, 15, 1, 45, 45, 45, 45, 45, 26, 26, 1, 1, 2, 2, 2, 6, 15, 1, 1] 67 rigid atoms, others: [4, 37, 6, 7, 8, 9, 10, 11, 12, 13, 22, 38, 30, 31] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042664 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042664 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042664/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042664 Building REAL250005042665 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042665' /scratch/stefan/7921153/working/building/REAL250005042665 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types Protomer extracton resulted in 0 protomers Marking REAL250005042665 as failed and skipping /scratch/stefan/7921153/working /scratch/stefan/7921153 `/scratch/stefan/7921153/working/building/REAL250005042665' -> `/scratch/stefan/7921153/failed/REAL250005042665' Building REAL250005042666 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042666' /scratch/stefan/7921153/working/building/REAL250005042666 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042666 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042666/0 /scratch/stefan/7921153/working/building/REAL250005042666 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 776) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/776 `/scratch/stefan/7921153/working/3D/776' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)CO)C[C@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005042666.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042666.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042666/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042666 none C[C@@H]1CN(C(=O)CO)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [15, 15, 15, 15, 15, 15, 22, 22, 26, 15, 8, 15, 8, 1, 8, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 26, 26, 78, 15, 15, 8, 1] 78 rigid atoms, others: [32, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 165 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042666 none C[C@@H]1CN(C(=O)CO)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 5, 14, 1, 1, 1, 1, 6, 6, 6, 15, 15, 15, 15, 15, 2, 2, 2, 1, 1, 14, 14, 42, 1, 1, 6, 15] 78 rigid atoms, others: [0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 24, 25, 29, 30] set([32, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 31]) total number of confs: 119 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042666 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042666 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042666/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042666 Building REAL250005042667 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042667' /scratch/stefan/7921153/working/building/REAL250005042667 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042667 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042667/0 /scratch/stefan/7921153/working/building/REAL250005042667 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 777) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/777 `/scratch/stefan/7921153/working/3D/777' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042667.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042667/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042667 none CC(O)C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [25, 17, 25, 11, 17, 11, 11, 11, 11, 11, 6, 11, 6, 1, 6, 1, 1, 1, 1, 1, 1, 11, 25, 25, 25, 25, 75, 11, 11, 11, 11, 11, 7, 1, 11, 11] 75 rigid atoms, others: [33, 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, 34, 35]) total number of confs: 166 number of broken/clashed sets: 12 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042667 none CC(O)C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [14, 5, 14, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 11, 11, 11, 11, 11, 1, 14, 14, 14, 14, 42, 1, 1, 2, 2, 2, 6, 11, 1, 1] 75 rigid atoms, others: [34, 3, 5, 6, 7, 8, 9, 10, 11, 12, 35, 21, 27, 28] set([0, 1, 2, 4, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 114 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042667 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042667 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042667/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042667 Building REAL250005042668 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042668' /scratch/stefan/7921153/working/building/REAL250005042668 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042668 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042668/0 /scratch/stefan/7921153/working/building/REAL250005042668 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 778) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/778 `/scratch/stefan/7921153/working/3D/778' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2CC2F)C[C@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005042668.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042668/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042668 none C[C@@H]1CN(C(=O)C2CC2F)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 15, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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, 11, 11, 11, 14, 14, 28, 28, 28, 11, 6, 11, 6, 1, 6, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 28, 28, 28, 28, 11, 11, 6, 1] 28 rigid atoms, others: [35, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 81 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042668 none C[C@@H]1CN(C(=O)C2CC2F)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 15, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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: [15, 15, 15, 15, 8, 1, 8, 1, 1, 1, 1, 15, 15, 15, 15, 26, 26, 26, 28, 28, 28, 28, 28, 15, 15, 15, 15, 15, 1, 1, 1, 1, 15, 15, 26, 28] 28 rigid atoms, others: [5, 7, 8, 9, 10, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35]) total number of confs: 72 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042668 none C[C@@H]1CN(C(=O)C2CC2F)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 15, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 4, 4, 15, 15, 15, 1, 1, 1, 1, 6, 6, 6, 11, 11, 11, 11, 11, 2, 2, 2, 1, 1, 15, 15, 15, 15, 1, 1, 6, 11] 28 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 11, 12, 13, 14, 33, 26, 27] set([6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 34, 35]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042668 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042668 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042668/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042668 Building REAL250005042669 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042669' /scratch/stefan/7921153/working/building/REAL250005042669 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042669 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042669/0 /scratch/stefan/7921153/working/building/REAL250005042669 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 779) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/779 `/scratch/stefan/7921153/working/3D/779' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)CCF)C[C@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005042669.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042669/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042669 none C[C@@H]1CN(C(=O)CCF)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 15, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 12, 12, 12, 12, 25, 25, 51, 51, 12, 7, 12, 7, 1, 7, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 51, 51, 51, 51, 12, 12, 7, 1] 51 rigid atoms, others: [34, 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]) total number of confs: 180 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042669 none C[C@@H]1CN(C(=O)CCF)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 15, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 17, 27, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 12, 12, 2, 2, 2, 1, 1, 17, 17, 27, 27, 1, 1, 6, 12] 51 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 10, 11, 12, 13, 25, 26, 31] set([33, 34, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042669 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042669 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042669/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042669 Building REAL250005042670 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042670' /scratch/stefan/7921153/working/building/REAL250005042670 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042670 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042670/0 /scratch/stefan/7921153/working/building/REAL250005042670 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 780) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/780 `/scratch/stefan/7921153/working/3D/780' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C=CCF)C[C@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005042670.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042670.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042670/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042670 none C[C@@H]1CN(C(=O)C=CCF)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'F', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 5, 15, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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: [12, 12, 12, 12, 12, 12, 19, 19, 34, 34, 36, 12, 6, 12, 7, 1, 7, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 34, 34, 36, 36, 12, 12, 7, 1] 36 rigid atoms, others: [35, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 118 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042670 none C[C@@H]1CN(C(=O)C=CCF)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'F', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 5, 15, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 4, 4, 15, 15, 22, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 12, 12, 2, 2, 2, 1, 1, 15, 15, 22, 22, 1, 1, 6, 12] 36 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 11, 12, 13, 14, 33, 26, 27] set([6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 34, 35]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042670 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042670 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042670/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042670 Building REAL250005042671 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042671' /scratch/stefan/7921153/working/building/REAL250005042671 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042671 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042671/0 /scratch/stefan/7921153/working/building/REAL250005042671 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 781) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/781 `/scratch/stefan/7921153/working/3D/781' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042671.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042671.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042671/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042671 none C#CCCC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 65, 35, 14, 35, 14, 14, 14, 14, 14, 6, 14, 6, 1, 6, 1, 1, 1, 1, 1, 1, 14, 69, 69, 69, 65, 65, 14, 14, 14, 14, 14, 7, 1, 14, 14] 69 rigid atoms, others: [34, 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, 35, 36]) total number of confs: 250 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042671 none C#CCCC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [42, 41, 29, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 14, 14, 14, 14, 14, 1, 42, 41, 41, 29, 29, 1, 1, 2, 2, 2, 6, 14, 1, 1] 69 rigid atoms, others: [35, 4, 6, 7, 8, 9, 10, 11, 12, 13, 22, 36, 28, 29] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042671 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042671 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042671/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042671 Building REAL250005042672 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042672' /scratch/stefan/7921153/working/building/REAL250005042672 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042672 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042672/0 /scratch/stefan/7921153/working/building/REAL250005042672 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 782) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/782 `/scratch/stefan/7921153/working/3D/782' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2CCO2)C[C@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005042672.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042672.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042672/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042672 none C[C@@H]1CN(C(=O)C2CCO2)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [17, 17, 17, 17, 17, 17, 27, 27, 37, 37, 37, 17, 8, 17, 8, 1, 8, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 37, 37, 37, 37, 37, 17, 17, 9, 1] 37 rigid atoms, others: [36, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 115 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: REAL250005042672 none C[C@@H]1CN(C(=O)C2CCO2)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [22, 22, 22, 22, 10, 1, 10, 1, 1, 1, 1, 22, 22, 22, 22, 33, 33, 33, 37, 37, 37, 37, 37, 22, 22, 22, 22, 22, 1, 1, 1, 1, 1, 22, 22, 33, 37] 37 rigid atoms, others: [32, 5, 7, 8, 9, 10, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 33, 34, 35, 36]) total number of confs: 84 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042672 none C[C@@H]1CN(C(=O)C2CCO2)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 22, 22, 22, 1, 1, 1, 1, 6, 6, 6, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 22, 22, 22, 22, 22, 1, 1, 6, 17] 37 rigid atoms, others: [0, 1, 2, 3, 4, 5, 33, 11, 12, 34, 14, 13, 26, 27] set([6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 35, 36]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042672 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042672 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042672/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042672 Building REAL250005042673 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042673' /scratch/stefan/7921153/working/building/REAL250005042673 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042673 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042673/0 /scratch/stefan/7921153/working/building/REAL250005042673 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 783) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/783 `/scratch/stefan/7921153/working/3D/783' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C(C)(C)O)C[C@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005042673.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042673.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042673/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042673 none C[C@@H]1CN(C(=O)C(C)(C)O)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 11, 11, 11, 11, 21, 21, 26, 26, 26, 11, 5, 11, 5, 1, 5, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 26, 26, 26, 26, 26, 26, 78, 11, 11, 5, 1] 78 rigid atoms, others: [38, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 167 number of broken/clashed sets: 25 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042673 none C[C@@H]1CN(C(=O)C(C)(C)O)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 14, 14, 14, 1, 1, 1, 1, 6, 6, 6, 11, 11, 11, 11, 11, 2, 2, 2, 1, 1, 14, 14, 14, 14, 14, 14, 42, 1, 1, 6, 11] 78 rigid atoms, others: [0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 35, 36, 26, 27] set([6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 37, 38]) total number of confs: 123 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042673 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042673 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042673/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042673 Building REAL250005042674 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042674' /scratch/stefan/7921153/working/building/REAL250005042674 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042674 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042674/0 /scratch/stefan/7921153/working/building/REAL250005042674 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 784) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/784 `/scratch/stefan/7921153/working/3D/784' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC1C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042674.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042674.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042674/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042674 none CC1=CC1C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 26, 15, 26, 15, 15, 15, 15, 15, 8, 15, 8, 1, 8, 1, 1, 1, 1, 1, 1, 15, 40, 40, 40, 40, 40, 15, 15, 15, 15, 15, 9, 1, 15, 15] 40 rigid atoms, others: [34, 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, 35, 36]) total number of confs: 119 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: REAL250005042674 none CC1=CC1C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 24, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 15, 15, 15, 15, 15, 1, 24, 24, 24, 24, 24, 1, 1, 2, 2, 2, 6, 15, 1, 1] 40 rigid atoms, others: [35, 4, 6, 7, 8, 9, 10, 11, 12, 13, 22, 36, 28, 29] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34]) total number of confs: 91 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042674 none CC1=CC1C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 9, 9, 24, 24, 24, 24, 24, 24, 24, 37, 37, 37, 40, 40, 40, 40, 40, 24, 2, 2, 2, 1, 1, 24, 24, 24, 24, 24, 37, 40, 24, 24] 40 rigid atoms, others: [0, 1, 2, 3, 4, 26, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042674 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042674 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042674/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042674 Building REAL250005042675 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042675' /scratch/stefan/7921153/working/building/REAL250005042675 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042675 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042675/0 /scratch/stefan/7921153/working/building/REAL250005042675 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 785) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/785 `/scratch/stefan/7921153/working/3D/785' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](O)C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042675.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042675.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042675/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042675 none C[C@@H](O)C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [24, 16, 24, 24, 11, 16, 11, 11, 11, 11, 11, 5, 11, 5, 1, 5, 1, 1, 1, 1, 1, 1, 11, 24, 24, 24, 72, 11, 11, 11, 11, 11, 6, 1, 11, 11] 72 rigid atoms, others: [33, 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, 34, 35]) total number of confs: 160 number of broken/clashed sets: 12 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042675 none C[C@@H](O)C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [13, 6, 13, 13, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 11, 11, 11, 11, 11, 1, 13, 13, 13, 39, 1, 1, 2, 2, 2, 6, 11, 1, 1] 72 rigid atoms, others: [34, 35, 4, 6, 7, 8, 9, 10, 11, 12, 13, 22, 27, 28] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 108 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042675 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042675 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042675/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042675 Building REAL250005042676 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042676' /scratch/stefan/7921153/working/building/REAL250005042676 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042676 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042676/0 /scratch/stefan/7921153/working/building/REAL250005042676 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 786) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/786 `/scratch/stefan/7921153/working/3D/786' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C=CCO)C[C@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005042676.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042676.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042676/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042676 none C[C@@H]1CN(C(=O)C=CCO)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 5, 12, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [20, 20, 20, 20, 20, 20, 35, 35, 63, 63, 66, 20, 8, 20, 9, 1, 9, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 63, 63, 66, 66, 198, 20, 20, 9, 1] 198 rigid atoms, others: [36, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 402 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042676 none C[C@@H]1CN(C(=O)C=CCO)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 5, 12, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 198 conformations in input total number of sets (complete confs): 198 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 27, 27, 52, 1, 1, 1, 1, 6, 6, 6, 20, 20, 20, 20, 20, 2, 2, 2, 1, 1, 27, 27, 52, 52, 156, 1, 1, 6, 20] 198 rigid atoms, others: [0, 1, 2, 3, 4, 5, 33, 11, 12, 34, 14, 13, 26, 27] set([6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 35, 36]) total number of confs: 379 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042676 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042676 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042676/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042676 Building REAL250005042677 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042677' /scratch/stefan/7921153/working/building/REAL250005042677 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042677 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042677/0 /scratch/stefan/7921153/working/building/REAL250005042677 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 787) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/787 `/scratch/stefan/7921153/working/3D/787' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2=CCC2)C[C@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005042677.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042677.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042677/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042677 none C[C@@H]1CN(C(=O)C2=CCC2)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 14, 14, 24, 24, 24, 24, 24, 14, 8, 14, 8, 1, 8, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 24, 24, 24, 24, 24, 14, 14, 8, 1] 24 rigid atoms, others: [36, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 71 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: REAL250005042677 none C[C@@H]1CN(C(=O)C2=CCC2)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 8, 1, 8, 1, 1, 1, 1, 16, 16, 16, 16, 23, 23, 23, 24, 24, 24, 24, 24, 16, 16, 16, 16, 16, 1, 1, 1, 1, 1, 16, 16, 23, 24] 24 rigid atoms, others: [32, 5, 7, 8, 9, 10, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 33, 34, 35, 36]) total number of confs: 55 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042677 none C[C@@H]1CN(C(=O)C2=CCC2)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 7, 16, 16, 16, 1, 1, 1, 1, 6, 6, 6, 14, 14, 14, 14, 14, 2, 2, 2, 1, 1, 16, 16, 16, 16, 16, 1, 1, 6, 14] 24 rigid atoms, others: [0, 1, 2, 3, 4, 5, 33, 11, 12, 34, 14, 13, 26, 27] set([6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 35, 36]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042677 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042677 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042677/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042677 Building REAL250005042678 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042678' /scratch/stefan/7921153/working/building/REAL250005042678 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042678 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042678/0 /scratch/stefan/7921153/working/building/REAL250005042678 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 788) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/788 `/scratch/stefan/7921153/working/3D/788' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CON=CC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042678.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042678.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042678/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042678 none CON=CC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 8, 1, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 34, 14, 34, 14, 14, 14, 14, 14, 7, 14, 7, 1, 7, 1, 1, 1, 1, 1, 1, 14, 56, 56, 56, 56, 14, 14, 14, 14, 14, 7, 1, 14, 14] 56 rigid atoms, others: [33, 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, 34, 35]) total number of confs: 165 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042678 none CON=CC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 8, 1, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [36, 31, 31, 7, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 14, 14, 14, 14, 14, 1, 36, 36, 36, 31, 1, 1, 2, 2, 2, 6, 14, 1, 1] 56 rigid atoms, others: [34, 35, 4, 6, 7, 8, 9, 10, 11, 12, 13, 22, 27, 28] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042678 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042678 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042678/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042678 Building REAL250005042679 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042679' /scratch/stefan/7921153/working/building/REAL250005042679 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042679 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042679/0 /scratch/stefan/7921153/working/building/REAL250005042679 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 789) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/789 `/scratch/stefan/7921153/working/3D/789' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2(F)CC2)C[C@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005042679.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042679.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042679/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042679 none C[C@@H]1CN(C(=O)C2(F)CC2)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 15, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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, 11, 11, 11, 20, 20, 31, 31, 31, 11, 7, 11, 7, 1, 7, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 31, 31, 31, 31, 11, 11, 7, 1] 31 rigid atoms, others: [35, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 101 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: REAL250005042679 none C[C@@H]1CN(C(=O)C2(F)CC2)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 15, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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: [18, 18, 18, 18, 8, 1, 8, 1, 1, 1, 1, 18, 18, 18, 18, 29, 29, 29, 31, 31, 31, 31, 31, 18, 18, 18, 18, 18, 1, 1, 1, 1, 18, 18, 29, 31] 31 rigid atoms, others: [5, 7, 8, 9, 10, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35]) total number of confs: 74 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042679 none C[C@@H]1CN(C(=O)C2(F)CC2)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 15, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 18, 18, 18, 1, 1, 1, 1, 6, 6, 6, 11, 11, 11, 11, 11, 2, 2, 2, 1, 1, 18, 18, 18, 18, 1, 1, 6, 11] 31 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 11, 12, 13, 14, 33, 26, 27] set([6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 34, 35]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042679 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042679 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042679/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042679 Building REAL250005042680 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042680' /scratch/stefan/7921153/working/building/REAL250005042680 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042680 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042680/0 /scratch/stefan/7921153/working/building/REAL250005042680 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 790) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/790 `/scratch/stefan/7921153/working/3D/790' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=C(F)C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042680.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042680.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042680/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042680 none CC=C(F)C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 15, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 21, 32, 11, 21, 11, 11, 11, 11, 11, 6, 11, 6, 1, 6, 1, 1, 1, 1, 1, 1, 11, 32, 32, 32, 32, 11, 11, 11, 11, 11, 6, 1, 11, 11] 32 rigid atoms, others: [33, 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, 34, 35]) total number of confs: 95 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042680 none CC=C(F)C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 15, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [24, 23, 6, 24, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 11, 11, 11, 11, 11, 1, 24, 24, 24, 23, 1, 1, 2, 2, 2, 6, 11, 1, 1] 32 rigid atoms, others: [34, 35, 4, 6, 7, 8, 9, 10, 11, 12, 13, 22, 27, 28] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042680 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042680 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042680/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042680 Building REAL250005042681 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042681' /scratch/stefan/7921153/working/building/REAL250005042681 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042681 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042681/0 /scratch/stefan/7921153/working/building/REAL250005042681 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 791) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/791 `/scratch/stefan/7921153/working/3D/791' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CO)C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042681.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042681.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042681/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042681 none CC(CO)C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [28, 20, 28, 29, 10, 20, 10, 10, 10, 10, 10, 3, 10, 3, 1, 3, 1, 1, 1, 1, 1, 1, 10, 28, 28, 28, 28, 29, 29, 87, 10, 10, 10, 10, 10, 4, 1, 10, 10] 87 rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 195 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042681 none CC(CO)C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [14, 5, 14, 21, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 10, 10, 10, 10, 10, 1, 14, 14, 14, 14, 21, 21, 63, 1, 1, 2, 2, 2, 6, 10, 1, 1] 87 rigid atoms, others: [4, 37, 6, 7, 8, 9, 10, 11, 12, 13, 22, 38, 30, 31] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36]) total number of confs: 170 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042681 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042681 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042681/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042681 Building REAL250005042682 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042682' /scratch/stefan/7921153/working/building/REAL250005042682 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042682 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042682/0 /scratch/stefan/7921153/working/building/REAL250005042682 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 792) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/792 `/scratch/stefan/7921153/working/3D/792' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](O)C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042682.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042682.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042682/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042682 none C[C@H](O)C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [24, 16, 24, 24, 12, 16, 12, 12, 12, 12, 12, 8, 12, 8, 1, 8, 1, 1, 1, 1, 1, 1, 12, 24, 24, 24, 72, 12, 12, 12, 12, 12, 8, 1, 12, 12] 72 rigid atoms, others: [33, 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, 34, 35]) total number of confs: 155 number of broken/clashed sets: 15 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042682 none C[C@H](O)C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [12, 5, 12, 12, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 12, 12, 1, 12, 12, 12, 36, 1, 1, 2, 2, 2, 6, 12, 1, 1] 72 rigid atoms, others: [34, 35, 4, 6, 7, 8, 9, 10, 11, 12, 13, 22, 27, 28] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 101 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042682 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042682 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042682/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042682 Building REAL250005042683 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042683' /scratch/stefan/7921153/working/building/REAL250005042683 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042683 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042683/0 /scratch/stefan/7921153/working/building/REAL250005042683 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 793) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/793 `/scratch/stefan/7921153/working/3D/793' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C1CC1C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042683.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042683/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042683 none C=C1CC1C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 23, 15, 23, 15, 15, 15, 15, 15, 7, 15, 7, 1, 7, 1, 1, 1, 1, 1, 1, 15, 38, 38, 38, 38, 38, 15, 15, 15, 15, 15, 7, 1, 15, 15] 38 rigid atoms, others: [34, 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, 35, 36]) total number of confs: 117 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: REAL250005042683 none C=C1CC1C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [18, 18, 18, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 15, 15, 15, 15, 15, 1, 18, 18, 18, 18, 18, 1, 1, 2, 2, 2, 6, 15, 1, 1] 38 rigid atoms, others: [35, 4, 6, 7, 8, 9, 10, 11, 12, 13, 22, 36, 28, 29] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34]) total number of confs: 75 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042683 none C=C1CC1C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 8, 8, 18, 18, 18, 18, 18, 18, 18, 34, 34, 34, 38, 38, 38, 38, 38, 18, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18, 34, 38, 18, 18] 38 rigid atoms, others: [0, 1, 2, 3, 4, 23, 24, 25, 26, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042683 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042683 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042683/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042683 Building REAL250005042684 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042684' /scratch/stefan/7921153/working/building/REAL250005042684 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042684 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042684/0 /scratch/stefan/7921153/working/building/REAL250005042684 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 794) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/794 `/scratch/stefan/7921153/working/3D/794' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CF)C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042684.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042684/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042684 none CC(CF)C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [29, 21, 29, 31, 10, 21, 10, 10, 10, 10, 10, 5, 10, 5, 1, 5, 1, 1, 1, 1, 1, 1, 10, 29, 29, 29, 29, 31, 31, 10, 10, 10, 10, 10, 6, 1, 10, 10] 31 rigid atoms, others: [35, 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, 36, 37]) total number of confs: 117 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042684 none CC(CF)C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 10, 23, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 10, 10, 10, 10, 10, 1, 10, 10, 10, 10, 23, 23, 1, 1, 2, 2, 2, 6, 10, 1, 1] 31 rigid atoms, others: [4, 37, 6, 7, 8, 9, 10, 11, 12, 13, 22, 36, 29, 30] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042684 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042684 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042684/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042684 Building REAL250005042685 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042685' /scratch/stefan/7921153/working/building/REAL250005042685 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042685 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042685/0 /scratch/stefan/7921153/working/building/REAL250005042685 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 795) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/795 `/scratch/stefan/7921153/working/3D/795' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C(C)CC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042685.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042685.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042685/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042685 none C=C(C)CC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 69, 70, 36, 15, 36, 15, 15, 15, 15, 15, 7, 15, 7, 1, 7, 1, 1, 1, 1, 1, 1, 15, 70, 70, 70, 70, 70, 69, 69, 15, 15, 15, 15, 15, 7, 1, 15, 15] 70 rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 249 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042685 none C=C(C)CC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [45, 30, 45, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 15, 15, 15, 15, 15, 1, 45, 45, 45, 45, 45, 30, 30, 1, 1, 2, 2, 2, 6, 15, 1, 1] 70 rigid atoms, others: [4, 37, 6, 7, 8, 9, 10, 11, 12, 13, 22, 38, 30, 31] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042685 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042685 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042685/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042685 Building REAL250005042686 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042686' /scratch/stefan/7921153/working/building/REAL250005042686 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042686 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042686/0 /scratch/stefan/7921153/working/building/REAL250005042686 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 796) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/796 `/scratch/stefan/7921153/working/3D/796' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=CC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042686.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042686.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042686/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042686 none CC=CC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 21, 14, 21, 14, 14, 14, 14, 14, 7, 14, 7, 1, 7, 1, 1, 1, 1, 1, 1, 14, 27, 27, 27, 27, 27, 14, 14, 14, 14, 14, 7, 1, 14, 14] 27 rigid atoms, others: [33, 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, 34, 35]) total number of confs: 79 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042686 none CC=CC(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [15, 14, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 14, 14, 14, 14, 14, 1, 15, 15, 15, 14, 15, 1, 1, 2, 2, 2, 6, 14, 1, 1] 27 rigid atoms, others: [34, 3, 5, 6, 7, 8, 9, 10, 11, 12, 35, 21, 27, 28] set([0, 1, 2, 4, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042686 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042686 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042686/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042686 Building REAL250005042687 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042687' /scratch/stefan/7921153/working/building/REAL250005042687 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042687 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042687/0 /scratch/stefan/7921153/working/building/REAL250005042687 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 797) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/797 `/scratch/stefan/7921153/working/3D/797' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H]1C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005042687.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042687.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042687/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042687 none C[C@@H]1C[C@H]1C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 23, 33, 14, 23, 14, 14, 14, 14, 14, 8, 14, 8, 1, 8, 1, 1, 1, 1, 1, 1, 14, 33, 33, 33, 33, 33, 14, 14, 14, 14, 14, 8, 1, 14, 14] 33 rigid atoms, others: [36, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 101 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: REAL250005042687 none C[C@@H]1C[C@H]1C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 7, 19, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 14, 14, 14, 14, 14, 1, 19, 19, 19, 19, 19, 1, 1, 2, 2, 2, 6, 14, 1, 1] 33 rigid atoms, others: [37, 6, 8, 9, 10, 11, 12, 13, 14, 15, 24, 38, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36]) total number of confs: 79 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042687 none C[C@@H]1C[C@H]1C(=O)N1C[C@@H](C)[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 8, 8, 19, 19, 19, 19, 19, 19, 19, 30, 30, 30, 33, 33, 33, 33, 33, 19, 2, 2, 2, 1, 1, 19, 19, 19, 19, 19, 30, 33, 19, 19] 33 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042687 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042687 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042687/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042687 Building REAL250005042688 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042688' /scratch/stefan/7921153/working/building/REAL250005042688 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042688 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042688/0 /scratch/stefan/7921153/working/building/REAL250005042688 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 798) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/798 `/scratch/stefan/7921153/working/3D/798' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2(O)CC2)C[C@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005042688.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042688.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042688/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042688 none C[C@@H]1CN(C(=O)C2(O)CC2)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [12, 12, 12, 12, 12, 12, 19, 19, 29, 29, 29, 12, 8, 12, 8, 1, 8, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 87, 29, 29, 29, 29, 12, 12, 8, 1] 87 rigid atoms, others: [36, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 178 number of broken/clashed sets: 16 ./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: REAL250005042688 none C[C@@H]1CN(C(=O)C2(O)CC2)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [15, 15, 15, 15, 8, 1, 8, 1, 1, 1, 1, 15, 15, 15, 15, 25, 25, 25, 29, 29, 29, 29, 29, 15, 15, 15, 15, 15, 6, 1, 1, 1, 1, 15, 15, 25, 29] 87 rigid atoms, others: [32, 5, 7, 8, 9, 10, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36]) total number of confs: 76 number of broken/clashed sets: 16 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042688 none C[C@@H]1CN(C(=O)C2(O)CC2)C[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 87 conformations in input total number of sets (complete confs): 87 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 15, 15, 15, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 12, 12, 2, 2, 2, 1, 1, 45, 15, 15, 15, 15, 1, 1, 6, 12] 87 rigid atoms, others: [0, 1, 2, 3, 4, 5, 33, 11, 12, 34, 14, 13, 26, 27] set([6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 35, 36]) total number of confs: 110 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042688 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042688 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042688/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042688 Building REAL250005042689 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042689' /scratch/stefan/7921153/working/building/REAL250005042689 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042689 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042689/0 /scratch/stefan/7921153/working/building/REAL250005042689 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 799) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/799 `/scratch/stefan/7921153/working/3D/799' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)CC1CC1) `REAL250005042689.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042689.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042689/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042689 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)CC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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] 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: [70, 70, 70, 70, 70, 70, 115, 115, 141, 141, 141, 141, 141, 70, 23, 70, 23, 3, 23, 1, 1, 1, 1, 70, 70, 70, 70, 70, 141, 70, 70, 23, 3, 3, 1, 1, 1, 1, 1] 141 rigid atoms, others: [34, 35, 36, 37, 38, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 391 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: REAL250005042689 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)CC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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] 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: [28, 28, 28, 28, 9, 1, 9, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 61, 61, 61, 118, 141, 141, 28, 28, 28, 28, 28, 1, 28, 28, 61, 118, 118, 141, 141, 141, 141, 141] 141 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 514 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042689 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)CC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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] 0 hydrogens need rotated 141 conformations in input total number of sets (complete confs): 141 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 7, 28, 28, 28, 28, 28, 1, 1, 1, 1, 6, 6, 6, 46, 70, 70, 2, 2, 2, 1, 1, 28, 1, 1, 6, 46, 46, 70, 70, 70, 70, 70] 141 rigid atoms, others: [0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 26, 27, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 290 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042689 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042689 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042689/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042689 Building REAL250005042690 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042690' /scratch/stefan/7921153/working/building/REAL250005042690 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042690 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042690/0 /scratch/stefan/7921153/working/building/REAL250005042690 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 800) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/800 `/scratch/stefan/7921153/working/3D/800' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C(C)(C)F) `REAL250005042690.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042690.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042690/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042690 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C(C)(C)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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] 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: [24, 24, 24, 24, 10, 1, 10, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 50, 50, 50, 67, 67, 67, 24, 24, 24, 24, 24, 1, 24, 24, 50, 67, 67, 67, 67, 67, 67] 67 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 211 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042690 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C(C)(C)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 5, 24, 24, 24, 24, 24, 1, 1, 1, 1, 6, 6, 6, 33, 33, 33, 2, 2, 2, 1, 1, 24, 1, 1, 6, 33, 33, 33, 33, 33, 33] 67 rigid atoms, others: [0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 26, 27, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042690 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042690 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042690/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042690 Building REAL250005042691 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042691' /scratch/stefan/7921153/working/building/REAL250005042691 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042691 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042691/0 /scratch/stefan/7921153/working/building/REAL250005042691 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 801) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/801 `/scratch/stefan/7921153/working/3D/801' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005042691.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042691.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042691/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042691 none COCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [94, 94, 61, 61, 61, 24, 24, 24, 24, 9, 1, 9, 1, 1, 1, 1, 1, 1, 23, 23, 24, 23, 94, 94, 94, 94, 94, 61, 24, 24, 1, 23, 23, 24, 24, 24] 94 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35]) total number of confs: 336 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042691 none COCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [48, 34, 6, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 23, 24, 24, 24, 24, 1, 1, 1, 1, 48, 48, 48, 34, 34, 6, 1, 1, 23, 1, 1, 2, 2, 2] 94 rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 28, 29, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 30, 33, 34, 35]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042691 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042691 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042691/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042691 Building REAL250005042692 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042692' /scratch/stefan/7921153/working/building/REAL250005042692 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042692 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042692/0 /scratch/stefan/7921153/working/building/REAL250005042692 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 802) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/802 `/scratch/stefan/7921153/working/3D/802' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005042692.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042692/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042692 none CCCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 135, 73, 73, 73, 32, 32, 32, 32, 10, 1, 10, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 136, 136, 136, 136, 136, 135, 135, 73, 32, 32, 1, 32, 32, 32, 32, 32] 136 rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37]) total number of confs: 478 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042692 none CCCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [57, 37, 6, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 32, 32, 32, 32, 32, 1, 1, 1, 1, 67, 67, 67, 67, 67, 37, 37, 6, 1, 1, 32, 1, 1, 2, 2, 2] 136 rigid atoms, others: [33, 34, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 32, 35, 36, 37]) total number of confs: 390 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042692 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042692 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042692/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042692 Building REAL250005042693 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042693' /scratch/stefan/7921153/working/building/REAL250005042693 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042693 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042693/0 /scratch/stefan/7921153/working/building/REAL250005042693 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 803) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/803 `/scratch/stefan/7921153/working/3D/803' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005042693.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042693.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042693/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042693 none CC(C)CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [90, 88, 90, 48, 48, 48, 24, 24, 24, 24, 9, 1, 9, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 90, 90, 90, 90, 90, 90, 90, 88, 88, 48, 24, 24, 1, 24, 24, 24, 24, 24] 90 rigid atoms, others: [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, 34, 36, 37, 38, 39, 40]) total number of confs: 309 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042693 none CC(C)CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [28, 26, 35, 6, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 24, 24, 24, 24, 24, 1, 1, 1, 1, 35, 35, 35, 35, 35, 35, 35, 26, 26, 6, 1, 1, 24, 1, 1, 2, 2, 2] 90 rigid atoms, others: [33, 34, 36, 37, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 38, 39, 40]) total number of confs: 226 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042693 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042693 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042693/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042693 Building REAL250005042694 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042694' /scratch/stefan/7921153/working/building/REAL250005042694 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042694 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042694/0 /scratch/stefan/7921153/working/building/REAL250005042694 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 804) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/804 `/scratch/stefan/7921153/working/3D/804' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005042694.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042694/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042694 none CC1CC1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 49, 49, 49, 23, 24, 24, 23, 7, 1, 7, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 74, 74, 74, 74, 74, 74, 74, 49, 23, 23, 1, 24, 24, 24, 24, 24] 74 rigid atoms, others: [33, 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, 34, 35, 36, 37, 38]) total number of confs: 218 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: REAL250005042694 none CC1CC1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [31, 31, 31, 6, 6, 6, 1, 1, 1, 1, 1, 1, 5, 6, 24, 24, 24, 24, 24, 1, 1, 1, 1, 31, 31, 31, 31, 31, 31, 31, 6, 1, 1, 24, 1, 1, 2, 2, 2] 74 rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 33, 36, 37, 38]) total number of confs: 113 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042694 none CC1CC1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 10, 10, 10, 31, 31, 31, 31, 67, 67, 74, 74, 74, 74, 74, 31, 31, 31, 31, 2, 2, 2, 1, 1, 1, 1, 10, 31, 31, 74, 31, 31, 31, 31, 31] 74 rigid atoms, others: [0, 1, 2, 3, 4, 26, 27, 28, 29] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042694 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042694 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042694/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042694 Building REAL250005042695 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042695' /scratch/stefan/7921153/working/building/REAL250005042695 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042695 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042695/0 /scratch/stefan/7921153/working/building/REAL250005042695 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 805) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/805 `/scratch/stefan/7921153/working/3D/805' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005042695.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042695.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042695/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042695 none CCOCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 156 conformations in input total number of sets (complete confs): 156 using faster count positions algorithm for large data unique positions, atoms: [156, 156, 149, 75, 75, 75, 28, 28, 28, 28, 10, 1, 10, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 156, 156, 156, 156, 156, 149, 149, 75, 28, 28, 1, 28, 28, 28, 28, 28] 156 rigid atoms, others: [33, 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, 34, 35, 36, 37, 38]) total number of confs: 525 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042695 none CCOCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 156 conformations in input total number of sets (complete confs): 156 using faster count positions algorithm for large data unique positions, atoms: [99, 90, 42, 6, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 28, 28, 28, 28, 28, 1, 1, 1, 1, 99, 99, 99, 99, 99, 42, 42, 6, 1, 1, 28, 1, 1, 2, 2, 2] 156 rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 33, 36, 37, 38]) total number of confs: 307 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042695 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042695 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042695/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042695 Building REAL250005042696 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042696' /scratch/stefan/7921153/working/building/REAL250005042696 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042696 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042696/0 /scratch/stefan/7921153/working/building/REAL250005042696 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 806) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/806 `/scratch/stefan/7921153/working/3D/806' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)=CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005042696.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042696/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042696 none CC(C)=CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 5, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 49, 49, 49, 23, 23, 23, 23, 10, 1, 10, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 68, 68, 68, 68, 68, 68, 68, 49, 23, 23, 1, 23, 23, 23, 23, 23] 68 rigid atoms, others: [33, 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, 34, 35, 36, 37, 38]) total number of confs: 189 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042696 none CC(C)=CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 5, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [21, 21, 21, 5, 5, 5, 1, 1, 1, 1, 1, 1, 6, 6, 23, 23, 23, 23, 23, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 21, 5, 1, 1, 23, 1, 1, 2, 2, 2] 68 rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 33, 36, 37, 38]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042696 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042696 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042696/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042696 Building REAL250005042697 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042697' /scratch/stefan/7921153/working/building/REAL250005042697 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042697 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042697/0 /scratch/stefan/7921153/working/building/REAL250005042697 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 807) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/807 `/scratch/stefan/7921153/working/3D/807' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005042697.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042697/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042697 none CSCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 175 conformations in input total number of sets (complete confs): 175 using faster count positions algorithm for large data unique positions, atoms: [175, 162, 76, 76, 76, 28, 28, 28, 28, 9, 1, 9, 1, 1, 1, 1, 1, 1, 27, 27, 28, 27, 175, 175, 175, 162, 162, 76, 28, 28, 1, 27, 27, 28, 28, 28] 175 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35]) total number of confs: 618 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042697 none CSCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 175 conformations in input total number of sets (complete confs): 175 using faster count positions algorithm for large data unique positions, atoms: [103, 47, 6, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 27, 28, 28, 28, 28, 1, 1, 1, 1, 98, 103, 103, 47, 47, 6, 1, 1, 27, 1, 1, 2, 2, 2] 175 rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 28, 29, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 30, 33, 34, 35]) total number of confs: 292 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042697 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042697 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042697/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042697 Building REAL250005042698 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042698' /scratch/stefan/7921153/working/building/REAL250005042698 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042698 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042698/0 /scratch/stefan/7921153/working/building/REAL250005042698 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 808) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/808 `/scratch/stefan/7921153/working/3D/808' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005042698.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042698.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042698/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042698 none CCCCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 201, 184, 72, 72, 72, 29, 29, 29, 29, 10, 1, 10, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 200, 201, 201, 201, 201, 201, 201, 184, 184, 72, 29, 29, 1, 29, 29, 29, 29, 29] 201 rigid atoms, others: [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, 34, 36, 37, 38, 39, 40]) total number of confs: 764 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042698 none CCCCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 62, 41, 6, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 29, 29, 29, 29, 29, 1, 1, 1, 1, 104, 107, 107, 102, 101, 75, 75, 41, 41, 6, 1, 1, 29, 1, 1, 2, 2, 2] 201 rigid atoms, others: [33, 34, 36, 37, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 38, 39, 40]) total number of confs: 595 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042698 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042698 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042698/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042698 Building REAL250005042699 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042699' /scratch/stefan/7921153/working/building/REAL250005042699 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042699 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042699/0 /scratch/stefan/7921153/working/building/REAL250005042699 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 809) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/809 `/scratch/stefan/7921153/working/3D/809' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005042699.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042699.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042699/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042699 none CC(C)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 48, 67, 48, 48, 26, 26, 26, 26, 10, 1, 10, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 67, 67, 67, 67, 67, 67, 67, 48, 26, 26, 1, 26, 26, 26, 26, 26] 67 rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37]) total number of confs: 230 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042699 none CC(C)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [29, 6, 29, 6, 6, 1, 1, 1, 1, 1, 1, 5, 5, 26, 25, 26, 26, 26, 1, 1, 1, 1, 29, 29, 29, 29, 29, 29, 29, 6, 1, 1, 26, 1, 1, 2, 2, 2] 67 rigid atoms, others: [33, 34, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 32, 35, 36, 37]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042699 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042699 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042699/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042699 Building REAL250005042700 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042700' /scratch/stefan/7921153/working/building/REAL250005042700 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042700 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042700/0 /scratch/stefan/7921153/working/building/REAL250005042700 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 810) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/810 `/scratch/stefan/7921153/working/3D/810' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005042700.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042700.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042700/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042700 none CCC(C)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [123, 122, 62, 122, 62, 62, 26, 26, 26, 26, 9, 1, 9, 1, 1, 1, 1, 1, 1, 25, 25, 26, 25, 123, 123, 123, 123, 123, 122, 122, 122, 122, 62, 26, 26, 1, 25, 25, 26, 26, 26] 123 rigid atoms, others: [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, 34, 36, 37, 38, 39, 40]) total number of confs: 449 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042700 none CCC(C)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [50, 37, 6, 37, 6, 6, 1, 1, 1, 1, 1, 1, 5, 5, 25, 26, 26, 26, 26, 1, 1, 1, 1, 53, 53, 53, 53, 53, 37, 37, 37, 37, 6, 1, 1, 25, 1, 1, 2, 2, 2] 123 rigid atoms, others: [33, 34, 36, 37, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 38, 39, 40]) total number of confs: 277 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042700 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042700 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042700/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042700 Building REAL250005042701 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042701' /scratch/stefan/7921153/working/building/REAL250005042701 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042701 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042701/0 /scratch/stefan/7921153/working/building/REAL250005042701 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 811) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/811 `/scratch/stefan/7921153/working/3D/811' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005042701.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042701.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042701/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042701 none COC(C)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 59, 40, 59, 40, 40, 17, 17, 18, 17, 9, 1, 9, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 60, 60, 60, 59, 59, 59, 59, 40, 18, 18, 1, 18, 18, 18, 18, 18] 60 rigid atoms, others: [33, 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, 34, 35, 36, 37, 38]) total number of confs: 199 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042701 none COC(C)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [37, 30, 6, 31, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 18, 18, 18, 18, 18, 1, 1, 1, 1, 37, 37, 37, 31, 31, 31, 31, 6, 1, 1, 18, 1, 1, 2, 2, 2] 60 rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 33, 36, 37, 38]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042701 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042701 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042701/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042701 Building REAL250005042702 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042702' /scratch/stefan/7921153/working/building/REAL250005042702 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042702 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042702/0 /scratch/stefan/7921153/working/building/REAL250005042702 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 812) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/812 `/scratch/stefan/7921153/working/3D/812' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005042702.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042702.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042702/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042702 none C=CCCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 179, 64, 64, 64, 24, 24, 24, 24, 8, 1, 8, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 201, 201, 201, 201, 201, 179, 179, 64, 24, 24, 1, 24, 24, 24, 24, 24] 201 rigid atoms, others: [33, 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, 34, 35, 36, 37, 38]) total number of confs: 767 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042702 none C=CCCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 77, 40, 6, 6, 6, 1, 1, 1, 1, 1, 1, 7, 7, 24, 24, 24, 24, 24, 1, 1, 1, 1, 126, 126, 126, 77, 77, 40, 40, 6, 1, 1, 24, 1, 1, 2, 2, 2] 201 rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 33, 36, 37, 38]) total number of confs: 541 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042702 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042702 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042702/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042702 Building REAL250005042703 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042703' /scratch/stefan/7921153/working/building/REAL250005042703 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042703 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042703/0 /scratch/stefan/7921153/working/building/REAL250005042703 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 813) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/813 `/scratch/stefan/7921153/working/3D/813' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C#N)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005042703.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042703.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042703/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042703 none CC(C#N)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.1', 'N.1', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [94, 51, 94, 94, 51, 51, 23, 24, 24, 23, 8, 1, 8, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 94, 94, 94, 94, 51, 23, 23, 1, 24, 24, 24, 24, 24] 94 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35]) total number of confs: 315 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042703 none CC(C#N)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.1', 'N.1', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [39, 6, 39, 39, 6, 6, 1, 1, 1, 1, 1, 1, 6, 7, 24, 24, 24, 24, 24, 1, 1, 1, 1, 39, 39, 39, 39, 6, 1, 1, 24, 1, 1, 2, 2, 2] 94 rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 28, 29, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 30, 33, 34, 35]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042703 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042703 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042703/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042703 Building REAL250005042704 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042704' /scratch/stefan/7921153/working/building/REAL250005042704 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042704 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042704/0 /scratch/stefan/7921153/working/building/REAL250005042704 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 814) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/814 `/scratch/stefan/7921153/working/3D/814' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=C(C)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005042704.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042704/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042704 none CC=C(C)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 43, 71, 43, 43, 22, 22, 22, 22, 10, 1, 10, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 71, 71, 71, 71, 71, 71, 71, 43, 22, 22, 1, 22, 22, 22, 22, 22] 71 rigid atoms, others: [33, 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, 34, 35, 36, 37, 38]) total number of confs: 196 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042704 none CC=C(C)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [38, 38, 6, 38, 6, 6, 1, 1, 1, 1, 1, 1, 5, 5, 22, 22, 22, 22, 22, 1, 1, 1, 1, 38, 38, 38, 38, 38, 38, 38, 6, 1, 1, 22, 1, 1, 2, 2, 2] 71 rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 33, 36, 37, 38]) total number of confs: 124 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042704 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042704 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042704/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042704 Building REAL250005042705 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042705' /scratch/stefan/7921153/working/building/REAL250005042705 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042705 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042705/0 /scratch/stefan/7921153/working/building/REAL250005042705 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 815) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/815 `/scratch/stefan/7921153/working/3D/815' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005042705.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042705.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042705/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042705 none CCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [59, 46, 46, 46, 26, 26, 26, 26, 10, 1, 10, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 59, 59, 59, 59, 59, 46, 26, 26, 1, 26, 26, 26, 26, 26] 59 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34]) total number of confs: 191 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042705 none CCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [39, 6, 6, 6, 1, 1, 1, 1, 1, 1, 5, 5, 26, 26, 26, 26, 26, 1, 1, 1, 1, 39, 39, 39, 39, 39, 6, 1, 1, 26, 1, 1, 2, 2, 2] 59 rigid atoms, others: [4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 27, 28, 30, 31] set([0, 1, 2, 3, 33, 32, 10, 11, 12, 13, 14, 15, 16, 34, 21, 22, 23, 24, 25, 26, 29]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042705 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042705 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042705/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042705 Building REAL250005042706 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042706' /scratch/stefan/7921153/working/building/REAL250005042706 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042706 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042706/0 /scratch/stefan/7921153/working/building/REAL250005042706 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 816) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/816 `/scratch/stefan/7921153/working/3D/816' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005042706.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042706.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042706/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042706 none COCCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 173, 83, 83, 83, 30, 30, 30, 30, 10, 1, 10, 1, 1, 1, 1, 1, 1, 29, 30, 30, 30, 191, 191, 191, 191, 191, 173, 173, 83, 30, 30, 1, 30, 30, 30, 30, 30] 191 rigid atoms, others: [33, 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, 34, 35, 36, 37, 38]) total number of confs: 723 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042706 none COCCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [111, 68, 37, 6, 6, 6, 1, 1, 1, 1, 1, 1, 7, 7, 30, 30, 30, 30, 30, 1, 1, 1, 1, 111, 111, 111, 68, 68, 37, 37, 6, 1, 1, 30, 1, 1, 2, 2, 2] 191 rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 33, 36, 37, 38]) total number of confs: 409 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042706 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042706 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042706/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042706 Building REAL250005042707 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042707' /scratch/stefan/7921153/working/building/REAL250005042707 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042707 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042707/0 /scratch/stefan/7921153/working/building/REAL250005042707 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 817) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/817 `/scratch/stefan/7921153/working/3D/817' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005042707.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042707.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042707/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042707 none CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 18, 18, 18, 18, 8, 1, 8, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 21, 21, 21, 21, 18, 18, 1, 18, 18, 18, 18, 18] 21 rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31]) total number of confs: 46 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042707 none CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 18, 18, 18, 18, 18, 1, 1, 1, 1, 6, 6, 6, 6, 1, 1, 18, 1, 1, 2, 2, 2] 21 rigid atoms, others: [3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 24, 25, 27, 28] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 26, 29, 30, 31]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042707 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042707 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042707/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042707 Building REAL250005042708 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042708' /scratch/stefan/7921153/working/building/REAL250005042708 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042708 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042708/0 /scratch/stefan/7921153/working/building/REAL250005042708 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 818) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/818 `/scratch/stefan/7921153/working/3D/818' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C1CC1) `REAL250005042708.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042708.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042708/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042708 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 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: [28, 28, 28, 28, 28, 28, 59, 59, 76, 76, 76, 76, 76, 28, 12, 28, 12, 1, 12, 1, 1, 1, 28, 28, 28, 28, 28, 76, 28, 28, 12, 1, 1, 1, 1, 1] 76 rigid atoms, others: [32, 33, 34, 35, 17, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 205 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: REAL250005042708 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 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: [26, 26, 26, 25, 9, 1, 9, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 47, 47, 47, 76, 76, 26, 26, 26, 25, 25, 1, 26, 26, 47, 76, 76, 76, 76, 76] 76 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 27] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 208 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042708 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 76 conformations in input total number of sets (complete confs): 76 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 25, 25, 25, 26, 26, 1, 1, 1, 1, 5, 5, 5, 28, 28, 2, 2, 2, 1, 1, 25, 1, 1, 5, 28, 28, 28, 28, 28] 76 rigid atoms, others: [0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 25, 26, 28, 29] set([6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 27, 30, 31, 32, 33, 34, 35]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042708 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042708 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042708/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042708 Building REAL250005042709 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042709' /scratch/stefan/7921153/working/building/REAL250005042709 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042709 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042709/0 /scratch/stefan/7921153/working/building/REAL250005042709 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 819) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/819 `/scratch/stefan/7921153/working/3D/819' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C1CCC1) `REAL250005042709.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042709.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042709/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042709 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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] 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: [32, 32, 32, 32, 32, 32, 65, 65, 77, 77, 77, 77, 77, 32, 12, 32, 12, 1, 12, 1, 1, 1, 1, 32, 32, 32, 32, 32, 77, 32, 32, 12, 1, 1, 1, 1, 1, 1, 1] 77 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 17, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 216 number of broken/clashed sets: 1 ./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: REAL250005042709 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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] 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: [20, 20, 20, 20, 9, 1, 9, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 41, 41, 41, 77, 77, 77, 20, 20, 20, 20, 20, 1, 20, 20, 41, 77, 77, 77, 77, 77, 77, 77] 77 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 213 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042709 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 20, 20, 20, 20, 20, 1, 1, 1, 1, 6, 6, 6, 32, 32, 32, 2, 2, 2, 1, 1, 20, 1, 1, 6, 32, 32, 32, 32, 32, 32, 32] 77 rigid atoms, others: [0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 26, 27, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 112 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042709 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042709 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042709/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042709 Building REAL250005042710 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042710' /scratch/stefan/7921153/working/building/REAL250005042710 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042710 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042710/0 /scratch/stefan/7921153/working/building/REAL250005042710 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 820) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/820 `/scratch/stefan/7921153/working/3D/820' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C(N)=O) `REAL250005042710.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042710/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042710 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 4, 6, 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: [18, 18, 18, 18, 8, 1, 8, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 32, 32, 32, 38, 38, 18, 18, 18, 18, 18, 1, 18, 18, 32, 38, 38] 38 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 27] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32]) total number of confs: 99 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042710 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 18, 18, 18, 18, 18, 1, 1, 1, 1, 6, 6, 6, 14, 14, 2, 2, 2, 1, 1, 18, 1, 1, 6, 14, 14] 38 rigid atoms, others: [0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 25, 26, 28, 29] set([32, 6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 27, 30, 31]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042710 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042710 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042710/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042710 Building REAL250005042711 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042711' /scratch/stefan/7921153/working/building/REAL250005042711 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042711 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042711/0 /scratch/stefan/7921153/working/building/REAL250005042711 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 821) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/821 `/scratch/stefan/7921153/working/3D/821' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C(C)(C)C) `REAL250005042711.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042711.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042711/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042711 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 9, 1, 9, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 30, 30, 30, 32, 32, 32, 21, 21, 21, 21, 21, 1, 21, 21, 30, 32, 32, 32, 32, 32, 32, 32, 32, 32] 32 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 84 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042711 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 5, 21, 21, 21, 21, 21, 1, 1, 1, 1, 5, 5, 5, 9, 9, 9, 2, 2, 2, 1, 1, 21, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9] 32 rigid atoms, others: [0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 26, 27, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042711 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042711 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042711/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042711 Building REAL250005042712 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042712' /scratch/stefan/7921153/working/building/REAL250005042712 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042712 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042712/0 /scratch/stefan/7921153/working/building/REAL250005042712 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 822) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/822 `/scratch/stefan/7921153/working/3D/822' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C1(C)CC1) `REAL250005042712.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042712/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042712 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C1(C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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] 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: [23, 23, 23, 23, 23, 23, 65, 65, 78, 78, 78, 78, 78, 23, 6, 23, 6, 1, 6, 1, 1, 1, 1, 23, 23, 23, 23, 23, 78, 23, 23, 6, 2, 2, 2, 1, 1, 1, 1] 78 rigid atoms, others: [35, 36, 37, 38, 17, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 212 number of broken/clashed sets: 4 ./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: REAL250005042712 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C1(C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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] 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: [26, 26, 26, 26, 7, 1, 7, 1, 1, 1, 1, 1, 1, 25, 25, 26, 25, 48, 48, 48, 78, 78, 78, 26, 26, 26, 26, 26, 1, 25, 25, 48, 78, 78, 78, 78, 78, 78, 78] 78 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 236 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042712 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C1(C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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] 0 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 25, 25, 26, 26, 26, 1, 1, 1, 1, 5, 5, 5, 23, 23, 23, 2, 2, 2, 1, 1, 25, 1, 1, 5, 23, 23, 23, 23, 23, 23, 23] 78 rigid atoms, others: [0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 26, 27, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 102 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042712 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042712 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042712/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042712 Building REAL250005042713 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042713' /scratch/stefan/7921153/working/building/REAL250005042713 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042713 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042713/0 /scratch/stefan/7921153/working/building/REAL250005042713 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 823) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/823 `/scratch/stefan/7921153/working/3D/823' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H]1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005042713.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042713/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042713 none C[C@@H]1C[C@H]1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [80, 80, 80, 80, 42, 80, 42, 42, 21, 21, 21, 21, 8, 1, 8, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 80, 80, 80, 80, 80, 42, 21, 21, 1, 21, 21, 21, 21, 21] 80 rigid atoms, others: [33, 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, 34, 35, 36, 37, 38]) total number of confs: 223 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: REAL250005042713 none C[C@@H]1C[C@H]1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 32, 32, 6, 32, 6, 6, 1, 1, 1, 1, 1, 1, 5, 5, 21, 21, 21, 21, 21, 1, 1, 1, 1, 32, 32, 32, 32, 32, 6, 1, 1, 21, 1, 1, 2, 2, 2] 80 rigid atoms, others: [32, 34, 35, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 33, 36, 37, 38]) total number of confs: 112 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042713 none C[C@@H]1C[C@H]1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 32, 32, 32, 32, 67, 67, 80, 80, 80, 80, 80, 32, 32, 32, 32, 2, 2, 2, 1, 1, 12, 32, 32, 80, 32, 32, 32, 32, 32] 80 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042713 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042713 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042713/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042713 Building REAL250005042714 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042714' /scratch/stefan/7921153/working/building/REAL250005042714 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042714 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042714/0 /scratch/stefan/7921153/working/building/REAL250005042714 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 824) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/824 `/scratch/stefan/7921153/working/3D/824' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(F)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005042714.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042714/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042714 none CCC(F)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 126, 75, 126, 75, 75, 31, 31, 31, 31, 10, 1, 10, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 138, 138, 138, 138, 138, 126, 75, 31, 31, 1, 31, 31, 31, 31, 31] 138 rigid atoms, others: [32, 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, 33, 34, 35, 36, 37]) total number of confs: 500 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042714 none CCC(F)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [60, 41, 6, 41, 6, 6, 1, 1, 1, 1, 1, 1, 7, 7, 31, 31, 31, 31, 31, 1, 1, 1, 1, 70, 70, 70, 70, 70, 41, 6, 1, 1, 31, 1, 1, 2, 2, 2] 138 rigid atoms, others: [33, 34, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 32, 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 /scratch/stefan/7921153/working/building/REAL250005042714 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042714 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042714/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042714 Building REAL250005042715 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042715' /scratch/stefan/7921153/working/building/REAL250005042715 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042715 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042715/0 /scratch/stefan/7921153/working/building/REAL250005042715 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 825) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/825 `/scratch/stefan/7921153/working/3D/825' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)CCCF) `REAL250005042715.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042715.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042715/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042715 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)CCCF NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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] 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: [20, 20, 20, 20, 6, 1, 6, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 54, 54, 54, 132, 134, 148, 20, 20, 20, 20, 20, 1, 20, 20, 54, 132, 132, 148, 148, 148, 148] 148 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 653 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042715 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)CCCF NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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] 0 hydrogens need rotated 148 conformations in input total number of sets (complete confs): 148 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 20, 20, 20, 20, 20, 1, 1, 1, 1, 6, 6, 6, 38, 44, 96, 2, 2, 2, 1, 1, 20, 1, 1, 6, 38, 38, 64, 64, 83, 88] 148 rigid atoms, others: [0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 26, 27, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 503 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042715 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042715 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042715/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042715 Building REAL250005042716 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042716' /scratch/stefan/7921153/working/building/REAL250005042716 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042716 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042716/0 /scratch/stefan/7921153/working/building/REAL250005042716 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 826) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/826 `/scratch/stefan/7921153/working/3D/826' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@@H]1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005042716.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042716/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042716 none C[C@H]1C[C@@H]1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 87 conformations in input total number of sets (complete confs): 87 using faster count positions algorithm for large data unique positions, atoms: [87, 87, 87, 87, 50, 87, 50, 50, 27, 27, 27, 26, 9, 1, 9, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 87, 87, 87, 87, 87, 50, 26, 26, 1, 27, 27, 27, 27, 27] 87 rigid atoms, others: [33, 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, 34, 35, 36, 37, 38]) total number of confs: 235 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: REAL250005042716 none C[C@H]1C[C@@H]1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 87 conformations in input total number of sets (complete confs): 87 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 32, 32, 5, 32, 5, 5, 1, 1, 1, 1, 1, 1, 6, 6, 27, 27, 27, 27, 26, 1, 1, 1, 1, 32, 32, 32, 32, 32, 5, 1, 1, 27, 1, 1, 2, 2, 2] 87 rigid atoms, others: [32, 34, 35, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 33, 36, 37, 38]) total number of confs: 119 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042716 none C[C@H]1C[C@@H]1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 87 conformations in input total number of sets (complete confs): 87 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 32, 32, 32, 32, 73, 73, 87, 87, 87, 87, 87, 32, 32, 32, 32, 2, 2, 2, 1, 1, 13, 32, 32, 87, 32, 32, 32, 32, 32] 87 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 241 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042716 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042716 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042716/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042716 Building REAL250005042717 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042717' /scratch/stefan/7921153/working/building/REAL250005042717 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042717 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042717/0 /scratch/stefan/7921153/working/building/REAL250005042717 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 827) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/827 `/scratch/stefan/7921153/working/3D/827' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)CO) `REAL250005042717.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042717/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042717 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)CO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [22, 22, 22, 22, 8, 1, 8, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 40, 40, 40, 41, 22, 22, 22, 22, 22, 1, 22, 22, 40, 41, 41, 123] 123 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 26] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32]) total number of confs: 232 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042717 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)CO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 7, 22, 22, 22, 22, 22, 1, 1, 1, 1, 6, 6, 6, 20, 2, 2, 2, 1, 1, 22, 1, 1, 6, 20, 20, 60] 123 rigid atoms, others: [0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 24, 25, 27, 28] set([32, 6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 26, 29, 30, 31]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042717 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042717 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042717/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042717 Building REAL250005042718 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042718' /scratch/stefan/7921153/working/building/REAL250005042718 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042718 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042718/0 /scratch/stefan/7921153/working/building/REAL250005042718 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 828) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/828 `/scratch/stefan/7921153/working/3D/828' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C1CCO1) `REAL250005042718.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042718.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042718/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042718 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C1CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 23, 23, 38, 38, 42, 42, 42, 42, 42, 23, 11, 23, 11, 1, 11, 1, 1, 1, 1, 23, 23, 23, 23, 23, 42, 23, 23, 11, 1, 1, 1, 1, 1] 42 rigid atoms, others: [32, 33, 34, 35, 36, 17, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 118 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: REAL250005042718 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C1CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 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: [21, 21, 21, 21, 9, 1, 9, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 33, 33, 33, 42, 42, 42, 21, 21, 21, 21, 21, 1, 21, 21, 33, 42, 42, 42, 42, 42] 42 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 109 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042718 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C1CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 7, 21, 21, 21, 21, 21, 1, 1, 1, 1, 6, 6, 6, 23, 23, 23, 2, 2, 2, 1, 1, 21, 1, 1, 6, 23, 23, 23, 23, 23] 42 rigid atoms, others: [0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 26, 27, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 31, 32, 33, 34, 35, 36]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042718 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042718 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042718/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042718 Building REAL250005042719 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042719' /scratch/stefan/7921153/working/building/REAL250005042719 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042719 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042719/0 /scratch/stefan/7921153/working/building/REAL250005042719 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 829) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/829 `/scratch/stefan/7921153/working/3D/829' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C1COC1) `REAL250005042719.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042719.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042719/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042719 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C1COC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 3, 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: [36, 36, 36, 36, 36, 36, 64, 64, 70, 70, 70, 70, 70, 36, 13, 36, 13, 1, 13, 1, 1, 1, 1, 36, 36, 36, 36, 36, 70, 36, 36, 13, 1, 1, 1, 1, 1] 70 rigid atoms, others: [32, 33, 34, 35, 36, 17, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 203 number of broken/clashed sets: 3 ./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: REAL250005042719 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C1COC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 3, 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: [18, 18, 18, 18, 9, 1, 9, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 39, 39, 39, 70, 70, 70, 18, 18, 18, 18, 18, 1, 18, 18, 39, 70, 70, 70, 70, 70] 70 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 191 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042719 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C1COC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 5, 18, 18, 18, 18, 18, 1, 1, 1, 1, 6, 6, 6, 36, 36, 36, 2, 2, 2, 1, 1, 18, 1, 1, 6, 36, 36, 36, 36, 36] 70 rigid atoms, others: [0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 26, 27, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 31, 32, 33, 34, 35, 36]) total number of confs: 115 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042719 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042719 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042719/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042719 Building REAL250005042720 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042720' /scratch/stefan/7921153/working/building/REAL250005042720 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042720 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042720/0 /scratch/stefan/7921153/working/building/REAL250005042720 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 830) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/830 `/scratch/stefan/7921153/working/3D/830' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C=CCO) `REAL250005042720.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042720.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042720/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042720 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C=CCO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 1, 1, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 333 conformations in input total number of sets (complete confs): 333 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 26, 26, 10, 1, 10, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 62, 62, 62, 109, 109, 111, 26, 26, 26, 26, 26, 1, 26, 26, 62, 109, 109, 111, 111, 333] 333 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 653 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042720 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C=CCO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 1, 1, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 333 conformations in input total number of sets (complete confs): 333 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 26, 26, 26, 26, 26, 1, 1, 1, 1, 6, 6, 6, 35, 35, 73, 2, 2, 2, 1, 1, 26, 1, 1, 6, 35, 35, 73, 73, 219] 333 rigid atoms, others: [0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 26, 27, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 31, 32, 33, 34, 35, 36]) total number of confs: 506 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042720 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042720 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042720/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042720 Building REAL250005042721 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042721' /scratch/stefan/7921153/working/building/REAL250005042721 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042721 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042721/0 /scratch/stefan/7921153/working/building/REAL250005042721 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 831) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/831 `/scratch/stefan/7921153/working/3D/831' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC=CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005042721.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042721.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042721/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042721 none CCC=CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 91, 91, 63, 63, 63, 27, 27, 27, 27, 10, 1, 10, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 119, 119, 119, 119, 119, 91, 91, 63, 27, 27, 1, 27, 27, 27, 27, 27] 119 rigid atoms, others: [33, 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, 34, 35, 36, 37, 38]) total number of confs: 435 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042721 none CCC=CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [56, 31, 31, 5, 5, 5, 1, 1, 1, 1, 1, 1, 6, 6, 27, 27, 27, 27, 27, 1, 1, 1, 1, 56, 56, 56, 56, 56, 31, 31, 5, 1, 1, 27, 1, 1, 2, 2, 2] 119 rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 33, 36, 37, 38]) total number of confs: 251 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042721 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042721 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042721/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042721 Building REAL250005042722 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042722' /scratch/stefan/7921153/working/building/REAL250005042722 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042722 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042722/0 /scratch/stefan/7921153/working/building/REAL250005042722 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 832) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/832 `/scratch/stefan/7921153/working/3D/832' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005042722.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042722/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042722 none C#CCCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 145 conformations in input total number of sets (complete confs): 145 using faster count positions algorithm for large data unique positions, atoms: [145, 145, 135, 66, 66, 66, 29, 29, 29, 29, 10, 1, 10, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 145, 145, 145, 135, 135, 66, 29, 29, 1, 29, 29, 29, 29, 29] 145 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 31] 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, 32, 33, 34, 35, 36]) total number of confs: 529 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042722 none C#CCCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 145 conformations in input total number of sets (complete confs): 145 using faster count positions algorithm for large data unique positions, atoms: [68, 68, 38, 6, 6, 6, 1, 1, 1, 1, 1, 1, 7, 7, 29, 29, 29, 29, 29, 1, 1, 1, 1, 68, 68, 68, 38, 38, 6, 1, 1, 29, 1, 1, 2, 2, 2] 145 rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 29, 30] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 31, 34, 35, 36]) total number of confs: 337 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042722 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042722 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042722/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042722 Building REAL250005042723 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042723' /scratch/stefan/7921153/working/building/REAL250005042723 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042723 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042723/0 /scratch/stefan/7921153/working/building/REAL250005042723 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 833) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/833 `/scratch/stefan/7921153/working/3D/833' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(O)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005042723.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042723/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042723 none C=CC(O)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 321 conformations in input total number of sets (complete confs): 321 using faster count positions algorithm for large data unique positions, atoms: [107, 107, 61, 107, 61, 61, 25, 25, 25, 25, 9, 1, 9, 1, 1, 1, 1, 1, 1, 24, 24, 25, 24, 107, 107, 107, 107, 321, 61, 25, 25, 1, 24, 24, 25, 25, 25] 321 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 31] 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, 32, 33, 34, 35, 36]) total number of confs: 703 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042723 none C=CC(O)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 321 conformations in input total number of sets (complete confs): 321 using faster count positions algorithm for large data unique positions, atoms: [53, 35, 6, 35, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 24, 24, 25, 25, 25, 1, 1, 1, 1, 53, 53, 53, 35, 105, 6, 1, 1, 24, 1, 1, 2, 2, 2] 321 rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 29, 30] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 31, 34, 35, 36]) total number of confs: 327 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042723 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042723 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042723/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042723 Building REAL250005042724 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042724' /scratch/stefan/7921153/working/building/REAL250005042724 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042724 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042724/0 /scratch/stefan/7921153/working/building/REAL250005042724 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 834) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/834 `/scratch/stefan/7921153/working/3D/834' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005042724.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042724.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042724/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042724 none CC(O)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [50, 39, 50, 39, 39, 25, 25, 26, 25, 9, 1, 9, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 50, 50, 50, 50, 150, 39, 25, 25, 1, 26, 26, 26, 26, 26] 150 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35]) total number of confs: 298 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042724 none CC(O)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [25, 6, 25, 6, 6, 1, 1, 1, 1, 1, 1, 6, 7, 26, 26, 26, 26, 26, 1, 1, 1, 1, 25, 25, 25, 25, 75, 6, 1, 1, 26, 1, 1, 2, 2, 2] 150 rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 28, 29, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 30, 33, 34, 35]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042724 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042724 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042724/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042724 Building REAL250005042725 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042725' /scratch/stefan/7921153/working/building/REAL250005042725 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042725 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042725/0 /scratch/stefan/7921153/working/building/REAL250005042725 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 835) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/835 `/scratch/stefan/7921153/working/3D/835' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005042725.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042725.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042725/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042725 none CC(=O)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [51, 41, 51, 41, 41, 21, 21, 21, 21, 10, 1, 10, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 51, 51, 51, 41, 21, 21, 1, 21, 21, 21, 21, 21] 51 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33]) total number of confs: 138 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042725 none CC(=O)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [22, 6, 22, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 21, 21, 21, 21, 21, 1, 1, 1, 1, 22, 22, 22, 6, 1, 1, 21, 1, 1, 2, 2, 2] 51 rigid atoms, others: [5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 26, 27, 29, 30] set([0, 1, 2, 3, 4, 33, 32, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 28, 31]) total number of confs: 91 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042725 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042725 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042725/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042725 Building REAL250005042726 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042726' /scratch/stefan/7921153/working/building/REAL250005042726 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042726 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042726/0 /scratch/stefan/7921153/working/building/REAL250005042726 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 836) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/836 `/scratch/stefan/7921153/working/3D/836' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C1(F)CC1) `REAL250005042726.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042726.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042726/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042726 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C1(F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 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: [37, 37, 37, 37, 37, 37, 70, 70, 81, 81, 81, 81, 81, 37, 12, 37, 12, 1, 12, 1, 1, 1, 1, 37, 37, 37, 37, 37, 81, 37, 37, 12, 1, 1, 1, 1] 81 rigid atoms, others: [32, 33, 34, 35, 17, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 223 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: REAL250005042726 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C1(F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 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: [27, 27, 27, 26, 9, 1, 9, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 58, 58, 58, 81, 81, 81, 27, 27, 27, 26, 26, 1, 27, 27, 58, 81, 81, 81, 81] 81 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 217 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042726 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C1(F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 26, 26, 26, 26, 26, 1, 1, 1, 1, 6, 6, 6, 37, 37, 37, 2, 2, 2, 1, 1, 27, 1, 1, 6, 37, 37, 37, 37] 81 rigid atoms, others: [0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 26, 27, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 31, 32, 33, 34, 35]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042726 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042726 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042726/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042726 Building REAL250005042727 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042727' /scratch/stefan/7921153/working/building/REAL250005042727 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042727 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042727/0 /scratch/stefan/7921153/working/building/REAL250005042727 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 837) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/837 `/scratch/stefan/7921153/working/3D/837' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=C(F)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005042727.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042727.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042727/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042727 none CC=C(F)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 15, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 34, 41, 34, 34, 21, 21, 21, 21, 10, 1, 10, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 41, 41, 41, 41, 34, 21, 21, 1, 21, 21, 21, 21, 21] 41 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35]) total number of confs: 106 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042727 none CC=C(F)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 15, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 6, 21, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 21, 21, 21, 21, 21, 1, 1, 1, 1, 23, 23, 23, 23, 6, 1, 1, 21, 1, 1, 2, 2, 2] 41 rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 28, 29, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 30, 33, 34, 35]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042727 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042727 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042727/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042727 Building REAL250005042728 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042728' /scratch/stefan/7921153/working/building/REAL250005042728 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042728 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042728/0 /scratch/stefan/7921153/working/building/REAL250005042728 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 838) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/838 `/scratch/stefan/7921153/working/3D/838' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CO)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005042728.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042728/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042728 none CC(CO)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 333 conformations in input total number of sets (complete confs): 333 using faster count positions algorithm for large data unique positions, atoms: [110, 57, 110, 111, 57, 57, 23, 23, 23, 23, 9, 1, 9, 1, 1, 1, 1, 1, 1, 22, 22, 23, 22, 110, 110, 110, 110, 111, 111, 333, 57, 23, 23, 1, 22, 22, 23, 23, 23] 333 rigid atoms, others: [33, 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, 34, 35, 36, 37, 38]) total number of confs: 731 number of broken/clashed sets: 46 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042728 none CC(CO)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 333 conformations in input total number of sets (complete confs): 333 using faster count positions algorithm for large data unique positions, atoms: [38, 6, 38, 63, 6, 6, 1, 1, 1, 1, 1, 1, 5, 5, 22, 23, 23, 23, 23, 1, 1, 1, 1, 38, 38, 38, 38, 63, 63, 189, 6, 1, 1, 22, 1, 1, 2, 2, 2] 333 rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 33, 36, 37, 38]) total number of confs: 485 number of broken/clashed sets: 46 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042728 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042728 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042728/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042728 Building REAL250005042729 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042729' /scratch/stefan/7921153/working/building/REAL250005042729 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042729 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042729/0 /scratch/stefan/7921153/working/building/REAL250005042729 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 839) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/839 `/scratch/stefan/7921153/working/3D/839' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C1(O)CC1) `REAL250005042729.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042729/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042729 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C1(O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 225 conformations in input total number of sets (complete confs): 225 using faster count positions algorithm for large data unique positions, atoms: [34, 34, 34, 34, 34, 34, 61, 61, 75, 75, 75, 75, 75, 34, 11, 34, 11, 1, 11, 1, 1, 1, 1, 34, 34, 34, 34, 34, 75, 34, 34, 11, 6, 1, 1, 1, 1] 225 rigid atoms, others: [33, 34, 35, 36, 17, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 216 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: REAL250005042729 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C1(O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 225 conformations in input total number of sets (complete confs): 225 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 25, 24, 8, 1, 8, 1, 1, 1, 1, 1, 1, 24, 25, 25, 25, 57, 57, 57, 75, 75, 75, 25, 25, 25, 24, 24, 1, 24, 24, 57, 225, 75, 75, 75, 75] 225 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 430 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042729 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C1(O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 225 conformations in input total number of sets (complete confs): 225 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 24, 24, 25, 24, 24, 1, 1, 1, 1, 5, 5, 5, 34, 34, 34, 2, 2, 2, 1, 1, 24, 1, 1, 5, 102, 34, 34, 34, 34] 225 rigid atoms, others: [0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 26, 27, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 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/7921153/working/building/REAL250005042729 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042729 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042729/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042729 Building REAL250005042730 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042730' /scratch/stefan/7921153/working/building/REAL250005042730 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042730 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042730/0 /scratch/stefan/7921153/working/building/REAL250005042730 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 840) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/840 `/scratch/stefan/7921153/working/3D/840' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C1=CCC1) `REAL250005042730.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042730.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042730/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042730 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C1=CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 12, 12, 12, 23, 23, 31, 31, 31, 31, 31, 12, 6, 12, 6, 1, 6, 1, 1, 1, 1, 12, 12, 12, 12, 12, 31, 12, 12, 6, 1, 1, 1, 1, 1] 31 rigid atoms, others: [32, 33, 34, 35, 36, 17, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 78 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: REAL250005042730 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C1=CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 7, 1, 7, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 31, 31, 31, 31, 31, 31, 19, 19, 19, 18, 18, 1, 18, 18, 31, 31, 31, 31, 31, 31] 31 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 84 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042730 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C1=CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 18, 18, 18, 18, 18, 1, 1, 1, 1, 5, 5, 5, 12, 12, 12, 2, 2, 2, 1, 1, 18, 1, 1, 5, 12, 12, 12, 12, 12] 31 rigid atoms, others: [0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 26, 27, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 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/7921153/working/building/REAL250005042730 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042730 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042730/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042730 Building REAL250005042731 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042731' /scratch/stefan/7921153/working/building/REAL250005042731 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042731 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042731/0 /scratch/stefan/7921153/working/building/REAL250005042731 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 841) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/841 `/scratch/stefan/7921153/working/3D/841' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CF)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005042731.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042731.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042731/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042731 none CC(CF)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [115, 56, 115, 117, 56, 56, 22, 22, 22, 22, 9, 1, 9, 1, 1, 1, 1, 1, 1, 21, 21, 22, 21, 115, 115, 115, 115, 117, 117, 56, 22, 22, 1, 21, 21, 22, 22, 22] 117 rigid atoms, others: [32, 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, 33, 34, 35, 36, 37]) total number of confs: 431 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042731 none CC(CF)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [37, 6, 37, 73, 6, 6, 1, 1, 1, 1, 1, 1, 5, 5, 21, 22, 22, 22, 22, 1, 1, 1, 1, 37, 37, 37, 37, 73, 73, 6, 1, 1, 21, 1, 1, 2, 2, 2] 117 rigid atoms, others: [33, 34, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 32, 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/7921153/working/building/REAL250005042731 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042731 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042731/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042731 Building REAL250005042732 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042732' /scratch/stefan/7921153/working/building/REAL250005042732 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042732 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042732/0 /scratch/stefan/7921153/working/building/REAL250005042732 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 842) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/842 `/scratch/stefan/7921153/working/3D/842' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005042732.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042732/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042732 none CC=CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 41, 41, 41, 23, 23, 23, 23, 10, 1, 10, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 50, 50, 50, 50, 50, 41, 23, 23, 1, 23, 23, 23, 23, 23] 50 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35]) total number of confs: 135 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042732 none CC=CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 6, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 23, 23, 23, 23, 23, 1, 1, 1, 1, 20, 20, 20, 20, 20, 6, 1, 1, 23, 1, 1, 2, 2, 2] 50 rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 28, 29, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 30, 33, 34, 35]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042732 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042732 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042732/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042732 Building REAL250005042733 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042733' /scratch/stefan/7921153/working/building/REAL250005042733 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042733 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042733/0 /scratch/stefan/7921153/working/building/REAL250005042733 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 843) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/843 `/scratch/stefan/7921153/working/3D/843' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C=CCF) `REAL250005042733.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042733.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042733/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042733 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C=CCF NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 1, 1, 5, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 97 conformations in input total number of sets (complete confs): 97 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 25, 25, 9, 1, 9, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 62, 62, 62, 97, 97, 97, 25, 25, 25, 25, 25, 1, 25, 25, 62, 97, 97, 97, 97] 97 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 279 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042733 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C=CCF NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 1, 1, 5, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 97 conformations in input total number of sets (complete confs): 97 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 5, 25, 25, 25, 25, 25, 1, 1, 1, 1, 6, 6, 6, 32, 32, 62, 2, 2, 2, 1, 1, 25, 1, 1, 6, 32, 32, 62, 62] 97 rigid atoms, others: [0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 26, 27, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 31, 32, 33, 34, 35]) total number of confs: 249 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042733 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042733 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042733/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042733 Building REAL250005042734 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042734' /scratch/stefan/7921153/working/building/REAL250005042734 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042734 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042734/0 /scratch/stefan/7921153/working/building/REAL250005042734 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 844) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/844 `/scratch/stefan/7921153/working/3D/844' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)CN=[N+]=[N-]) `REAL250005042734.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042734/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042734 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)CN=[N+]=[N-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.2', 'N.1', 'N.1', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 26, 26, 8, 1, 8, 1, 1, 1, 1, 1, 1, 25, 25, 26, 25, 69, 69, 69, 188, 201, 201, 26, 26, 26, 26, 26, 1, 25, 25, 69, 188, 188] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33]) total number of confs: 680 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042734 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)CN=[N+]=[N-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.2', 'N.1', 'N.1', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 7, 26, 26, 26, 26, 26, 1, 1, 1, 1, 5, 5, 5, 48, 145, 145, 2, 2, 2, 1, 1, 26, 1, 1, 5, 48, 48] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 26, 27, 29, 30] set([32, 33, 6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 31]) total number of confs: 329 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042734 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042734 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042734/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042734 Building REAL250005042735 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042735' /scratch/stefan/7921153/working/building/REAL250005042735 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042735 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042735/0 /scratch/stefan/7921153/working/building/REAL250005042735 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 845) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/845 `/scratch/stefan/7921153/working/3D/845' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](O)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005042735.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042735.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042735/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042735 none C[C@H](O)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 147 conformations in input total number of sets (complete confs): 147 using faster count positions algorithm for large data unique positions, atoms: [49, 36, 49, 49, 36, 36, 23, 23, 23, 23, 9, 1, 9, 1, 1, 1, 1, 1, 1, 22, 22, 23, 22, 49, 49, 49, 147, 36, 23, 23, 1, 22, 22, 23, 23, 23] 147 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35]) total number of confs: 309 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042735 none C[C@H](O)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 147 conformations in input total number of sets (complete confs): 147 using faster count positions algorithm for large data unique positions, atoms: [30, 6, 30, 30, 6, 6, 1, 1, 1, 1, 1, 1, 5, 5, 22, 23, 23, 23, 23, 1, 1, 1, 1, 30, 30, 30, 90, 6, 1, 1, 22, 1, 1, 2, 2, 2] 147 rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 28, 29, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 30, 33, 34, 35]) total number of confs: 227 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042735 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042735 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042735/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042735 Building REAL250005042736 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042736' /scratch/stefan/7921153/working/building/REAL250005042736 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042736 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042736/0 /scratch/stefan/7921153/working/building/REAL250005042736 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 846) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/846 `/scratch/stefan/7921153/working/3D/846' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CON=CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005042736.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042736.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042736/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042736 none CON=CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 8, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 30, 30, 30, 17, 17, 17, 17, 10, 1, 10, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 37, 37, 37, 37, 30, 17, 17, 1, 17, 17, 17, 17, 17] 37 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35]) total number of confs: 97 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042736 none CON=CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 8, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [26, 20, 20, 6, 6, 6, 1, 1, 1, 1, 1, 1, 5, 5, 17, 17, 17, 17, 17, 1, 1, 1, 1, 26, 26, 26, 20, 6, 1, 1, 17, 1, 1, 2, 2, 2] 37 rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 28, 29, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 30, 33, 34, 35]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042736 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042736 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042736/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042736 Building REAL250005042737 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042737' /scratch/stefan/7921153/working/building/REAL250005042737 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042737 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042737/0 /scratch/stefan/7921153/working/building/REAL250005042737 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 847) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/847 `/scratch/stefan/7921153/working/3D/847' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H]1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005042737.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042737.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042737/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042737 none C[C@@H]1C[C@H]1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [80, 80, 80, 80, 42, 80, 42, 42, 21, 21, 21, 21, 8, 1, 8, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 80, 80, 80, 80, 80, 42, 21, 21, 1, 21, 21, 21, 21, 21] 80 rigid atoms, others: [33, 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, 34, 35, 36, 37, 38]) total number of confs: 223 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: REAL250005042737 none C[C@@H]1C[C@H]1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 32, 32, 6, 32, 6, 6, 1, 1, 1, 1, 1, 1, 5, 5, 21, 21, 21, 21, 21, 1, 1, 1, 1, 32, 32, 32, 32, 32, 6, 1, 1, 21, 1, 1, 2, 2, 2] 80 rigid atoms, others: [32, 34, 35, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 33, 36, 37, 38]) total number of confs: 112 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042737 none C[C@@H]1C[C@H]1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 32, 32, 32, 32, 67, 67, 80, 80, 80, 80, 80, 32, 32, 32, 32, 2, 2, 2, 1, 1, 12, 32, 32, 80, 32, 32, 32, 32, 32] 80 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042737 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042737 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042737/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042737 Building REAL250005042738 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042738' /scratch/stefan/7921153/working/building/REAL250005042738 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042738 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042738/0 /scratch/stefan/7921153/working/building/REAL250005042738 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 848) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/848 `/scratch/stefan/7921153/working/3D/848' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C(C)(C)O) `REAL250005042738.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042738/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042738 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C(C)(C)O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 210 conformations in input total number of sets (complete confs): 210 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 26, 26, 10, 1, 10, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 56, 56, 56, 70, 70, 70, 26, 26, 26, 26, 26, 1, 26, 26, 56, 70, 70, 70, 70, 70, 70, 210] 210 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 421 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042738 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C(C)(C)O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 210 conformations in input total number of sets (complete confs): 210 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 26, 26, 26, 26, 26, 1, 1, 1, 1, 6, 6, 6, 29, 29, 28, 2, 2, 2, 1, 1, 26, 1, 1, 6, 29, 29, 29, 29, 29, 29, 87] 210 rigid atoms, others: [0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 26, 27, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042738 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042738 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042738/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042738 Building REAL250005042739 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042739' /scratch/stefan/7921153/working/building/REAL250005042739 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042739 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042739/0 /scratch/stefan/7921153/working/building/REAL250005042739 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 849) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/849 `/scratch/stefan/7921153/working/3D/849' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C(C)CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005042739.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042739.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042739/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042739 none C=C(C)CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 58, 58, 58, 26, 26, 26, 25, 9, 1, 9, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 111, 111, 111, 111, 111, 111, 111, 58, 25, 25, 1, 26, 26, 26, 26, 26] 111 rigid atoms, others: [33, 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, 34, 35, 36, 37, 38]) total number of confs: 388 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042739 none C=C(C)CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [60, 44, 60, 6, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 26, 26, 26, 26, 25, 1, 1, 1, 1, 60, 60, 60, 60, 60, 44, 44, 6, 1, 1, 26, 1, 1, 2, 2, 2] 111 rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 33, 36, 37, 38]) total number of confs: 244 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042739 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042739 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042739/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042739 Building REAL250005042740 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042740' /scratch/stefan/7921153/working/building/REAL250005042740 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042740 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042740/0 /scratch/stefan/7921153/working/building/REAL250005042740 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 850) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/850 `/scratch/stefan/7921153/working/3D/850' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005042740.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042740/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042740 none C=CCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 109 conformations in input total number of sets (complete confs): 109 using faster count positions algorithm for large data unique positions, atoms: [109, 109, 67, 67, 67, 26, 26, 26, 26, 9, 1, 9, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 109, 109, 109, 109, 109, 67, 26, 26, 1, 26, 26, 26, 26, 26] 109 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35]) total number of confs: 389 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042740 none C=CCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 109 conformations in input total number of sets (complete confs): 109 using faster count positions algorithm for large data unique positions, atoms: [72, 41, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 26, 26, 26, 26, 26, 1, 1, 1, 1, 72, 72, 72, 41, 41, 5, 1, 1, 26, 1, 1, 2, 2, 2] 109 rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 28, 29, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 30, 33, 34, 35]) total number of confs: 282 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042740 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042740 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042740/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042740 Building REAL250005042741 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042741' /scratch/stefan/7921153/working/building/REAL250005042741 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005042741 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042741/0 /scratch/stefan/7921153/working/building/REAL250005042741 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 851) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/851 `/scratch/stefan/7921153/working/3D/851' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C[NH+](C)C) `REAL250005042741.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042741.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042741/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042741 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C[NH+](C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 7, 1, 7, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 23, 23, 23, 30, 30, 30, 30, 10, 10, 10, 10, 10, 1, 10, 10, 23, 30, 30, 30, 30, 30, 30, 30, 30] 30 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 99 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042741 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C[NH+](C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 3, 3, 10, 10, 10, 10, 10, 1, 1, 1, 1, 6, 6, 6, 22, 24, 24, 24, 2, 2, 2, 1, 1, 10, 1, 1, 6, 22, 22, 24, 24, 24, 24, 24, 24] 30 rigid atoms, others: [0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 27, 28, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042741 /scratch/stefan/7921153/working /scratch/stefan/7921153 mkdir: created directory `1' /scratch/stefan/7921153/working/building/REAL250005042741/1 /scratch/stefan/7921153/working/building/REAL250005042741 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 1 (index: 852) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/852 `/scratch/stefan/7921153/working/3D/852' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)CN(C)C) `REAL250005042741.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005042741.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042741/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042741 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)CN(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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, 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: [24, 24, 24, 24, 10, 1, 10, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 57, 57, 57, 93, 95, 95, 24, 24, 24, 24, 24, 1, 24, 24, 57, 93, 93, 95, 95, 95, 95, 95, 95] 95 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 322 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042741 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)CN(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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, 7] 0 hydrogens need rotated 95 conformations in input total number of sets (complete confs): 95 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 24, 24, 24, 24, 24, 1, 1, 1, 1, 6, 6, 6, 33, 42, 42, 2, 2, 2, 1, 1, 24, 1, 1, 6, 33, 33, 42, 42, 42, 42, 42, 42] 95 rigid atoms, others: [0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 26, 27, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042741 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042741 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 1: /scratch/stefan/7921153/working/building/REAL250005042741/1.* 0: /scratch/stefan/7921153/working/building/REAL250005042741/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042741 Building REAL250005042742 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042742' /scratch/stefan/7921153/working/building/REAL250005042742 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042742 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042742/0 /scratch/stefan/7921153/working/building/REAL250005042742 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 853) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/853 `/scratch/stefan/7921153/working/3D/853' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)CC#N) `REAL250005042742.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042742/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042742 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)CC#N NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.1', 'N.1', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 22, 22, 8, 1, 8, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 52, 52, 52, 73, 73, 22, 22, 22, 22, 22, 1, 22, 22, 52, 73, 73] 73 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 27] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32]) total number of confs: 240 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042742 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)CC#N NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.1', 'N.1', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 7, 22, 22, 22, 22, 22, 1, 1, 1, 1, 5, 5, 5, 40, 40, 2, 2, 2, 1, 1, 22, 1, 1, 5, 40, 40] 73 rigid atoms, others: [0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 25, 26, 28, 29] set([32, 6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 27, 30, 31]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042742 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042742 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042742/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042742 Building REAL250005042743 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042743' /scratch/stefan/7921153/working/building/REAL250005042743 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042743 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042743/0 /scratch/stefan/7921153/working/building/REAL250005042743 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 854) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/854 `/scratch/stefan/7921153/working/3D/854' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C1CC1F) `REAL250005042743.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042743.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042743/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042743 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C1CC1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 79 conformations in input total number of sets (complete confs): 79 using faster count positions algorithm for large data unique positions, atoms: [31, 31, 31, 31, 31, 31, 73, 73, 79, 79, 79, 79, 79, 31, 12, 31, 12, 1, 12, 1, 1, 1, 1, 31, 31, 31, 31, 31, 79, 31, 31, 12, 1, 1, 1, 1] 79 rigid atoms, others: [32, 33, 34, 35, 17, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 229 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: REAL250005042743 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C1CC1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 79 conformations in input total number of sets (complete confs): 79 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 24, 24, 10, 1, 10, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 46, 46, 46, 79, 79, 79, 24, 24, 24, 24, 24, 1, 24, 24, 46, 79, 79, 79, 79] 79 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 214 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042743 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)C1CC1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 79 conformations in input total number of sets (complete confs): 79 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 24, 24, 24, 24, 24, 1, 1, 1, 1, 5, 5, 5, 31, 31, 31, 2, 2, 2, 1, 1, 24, 1, 1, 5, 31, 31, 31, 31] 79 rigid atoms, others: [0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 26, 27, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 31, 32, 33, 34, 35]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042743 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042743 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042743/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042743 Building REAL250005042744 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042744' /scratch/stefan/7921153/working/building/REAL250005042744 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042744 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042744/0 /scratch/stefan/7921153/working/building/REAL250005042744 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 855) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/855 `/scratch/stefan/7921153/working/3D/855' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)CCF) `REAL250005042744.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042744.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042744/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042744 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)CCF NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 121 conformations in input total number of sets (complete confs): 121 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 28, 28, 10, 1, 10, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 66, 66, 66, 121, 121, 28, 28, 28, 28, 28, 1, 28, 28, 66, 121, 121, 121, 121] 121 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 27] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 421 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042744 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1NC(=O)CCF NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 121 conformations in input total number of sets (complete confs): 121 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 28, 28, 28, 28, 28, 1, 1, 1, 1, 5, 5, 5, 34, 62, 2, 2, 2, 1, 1, 28, 1, 1, 5, 34, 34, 62, 62] 121 rigid atoms, others: [0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 25, 26, 28, 29] set([32, 33, 34, 6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 27, 30, 31]) total number of confs: 306 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042744 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042744 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042744/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042744 Building REAL250005042745 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042745' /scratch/stefan/7921153/working/building/REAL250005042745 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042745 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042745/0 /scratch/stefan/7921153/working/building/REAL250005042745 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 856) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/856 `/scratch/stefan/7921153/working/3D/856' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H](C)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005042745.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042745/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042745 none CO[C@H](C)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 54, 70, 70, 54, 54, 25, 25, 25, 25, 9, 1, 9, 1, 1, 1, 1, 1, 1, 24, 24, 25, 24, 70, 70, 70, 70, 70, 70, 54, 25, 25, 1, 24, 24, 25, 25, 25] 70 rigid atoms, others: [33, 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, 34, 35, 36, 37, 38]) total number of confs: 223 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042745 none CO[C@H](C)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [40, 30, 6, 31, 31, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 24, 25, 25, 25, 25, 1, 1, 1, 1, 40, 40, 40, 31, 31, 31, 6, 1, 1, 24, 1, 1, 2, 2, 2] 70 rigid atoms, others: [32, 34, 35, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 33, 36, 37, 38]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042745 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042745 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042745/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042745 Building REAL250005042746 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042746' /scratch/stefan/7921153/working/building/REAL250005042746 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042746 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042746/0 /scratch/stefan/7921153/working/building/REAL250005042746 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 857) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/857 `/scratch/stefan/7921153/working/3D/857' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](O)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005042746.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042746.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042746/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042746 none C[C@@H](O)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [50, 39, 50, 50, 39, 39, 26, 26, 26, 26, 9, 1, 9, 1, 1, 1, 1, 1, 1, 25, 25, 26, 25, 50, 50, 50, 150, 39, 26, 26, 1, 25, 25, 26, 26, 26] 150 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35]) total number of confs: 300 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042746 none C[C@@H](O)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [25, 6, 25, 25, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 25, 26, 26, 26, 26, 1, 1, 1, 1, 25, 25, 25, 75, 6, 1, 1, 25, 1, 1, 2, 2, 2] 150 rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 28, 29, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 30, 33, 34, 35]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042746 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042746 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042746/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042746 Building REAL250005042747 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042747' /scratch/stefan/7921153/working/building/REAL250005042747 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042747 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042747/0 /scratch/stefan/7921153/working/building/REAL250005042747 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 858) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/858 `/scratch/stefan/7921153/working/3D/858' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C1CC1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005042747.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042747/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042747 none C=C1CC1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 92 conformations in input total number of sets (complete confs): 92 using faster count positions algorithm for large data unique positions, atoms: [92, 92, 92, 48, 48, 48, 23, 23, 23, 23, 9, 1, 9, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 92, 92, 92, 92, 92, 48, 23, 23, 1, 23, 23, 23, 23, 23] 92 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 31] 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, 32, 33, 34, 35, 36]) total number of confs: 243 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: REAL250005042747 none C=C1CC1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 92 conformations in input total number of sets (complete confs): 92 using faster count positions algorithm for large data unique positions, atoms: [40, 40, 40, 6, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 23, 23, 23, 23, 23, 1, 1, 1, 1, 40, 40, 40, 40, 40, 6, 1, 1, 23, 1, 1, 2, 2, 2] 92 rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 29, 30] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 31, 34, 35, 36]) total number of confs: 131 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042747 none C=C1CC1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 92 conformations in input total number of sets (complete confs): 92 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 13, 13, 13, 40, 40, 40, 40, 75, 75, 92, 92, 92, 92, 92, 40, 40, 40, 40, 1, 1, 1, 1, 1, 13, 40, 40, 92, 40, 40, 40, 40, 40] 92 rigid atoms, others: [0, 1, 2, 3, 4, 23, 24, 25, 26, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 259 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042747 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042747 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042747/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042747 Building REAL250005042748 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042748' /scratch/stefan/7921153/working/building/REAL250005042748 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042748 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042748/0 /scratch/stefan/7921153/working/building/REAL250005042748 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 859) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/859 `/scratch/stefan/7921153/working/3D/859' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005042748.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042748/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042748 none CC1=CC1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 52, 52, 52, 28, 28, 28, 28, 10, 1, 10, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 100, 100, 100, 100, 100, 52, 28, 28, 1, 28, 28, 28, 28, 28] 100 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 31] 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, 32, 33, 34, 35, 36]) total number of confs: 270 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: REAL250005042748 none CC1=CC1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [45, 45, 45, 6, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 28, 28, 28, 28, 28, 1, 1, 1, 1, 45, 45, 45, 45, 45, 6, 1, 1, 28, 1, 1, 2, 2, 2] 100 rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 29, 30] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 31, 34, 35, 36]) total number of confs: 147 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042748 none CC1=CC1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 13, 13, 13, 45, 45, 45, 45, 82, 82, 100, 100, 100, 100, 100, 45, 45, 45, 45, 2, 2, 2, 1, 1, 13, 45, 45, 100, 45, 45, 45, 45, 45] 100 rigid atoms, others: [0, 1, 2, 3, 4, 26, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 281 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042748 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042748 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042748/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042748 Building REAL250005042749 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042749' /scratch/stefan/7921153/working/building/REAL250005042749 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042749 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042749/0 /scratch/stefan/7921153/working/building/REAL250005042749 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 860) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/860 `/scratch/stefan/7921153/working/3D/860' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005042749.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042749.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042749/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042749 none C=CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 42, 28, 28, 28, 28, 10, 1, 10, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 42, 42, 42, 42, 28, 28, 1, 28, 28, 28, 28, 28] 42 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32]) total number of confs: 98 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042749 none C=CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [18, 6, 6, 6, 1, 1, 1, 1, 1, 1, 6, 7, 28, 28, 28, 28, 28, 1, 1, 1, 1, 18, 18, 18, 6, 1, 1, 28, 1, 1, 2, 2, 2] 42 rigid atoms, others: [4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 25, 26, 28, 29] set([0, 1, 2, 3, 32, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 27, 30, 31]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042749 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042749 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042749/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042749 Building REAL250005042750 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042750' /scratch/stefan/7921153/working/building/REAL250005042750 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042750 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042750/0 /scratch/stefan/7921153/working/building/REAL250005042750 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 861) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/861 `/scratch/stefan/7921153/working/3D/861' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O) `REAL250005042750.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042750/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042750 none CCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [45, 36, 36, 36, 18, 19, 19, 18, 6, 1, 6, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 45, 45, 45, 45, 45, 36, 18, 18, 1, 19, 19, 57] 135 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32]) total number of confs: 199 number of broken/clashed sets: 15 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042750 none CCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [29, 6, 6, 6, 1, 1, 1, 1, 1, 1, 5, 5, 18, 18, 18, 19, 18, 1, 1, 1, 1, 29, 29, 29, 29, 29, 6, 1, 1, 18, 1, 1, 6] 135 rigid atoms, others: [4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 27, 28, 30, 31] set([0, 1, 2, 3, 32, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 29]) total number of confs: 134 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042750 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042750 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042750/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042750 Building REAL250005042751 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042751' /scratch/stefan/7921153/working/building/REAL250005042751 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042751 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042751/0 /scratch/stefan/7921153/working/building/REAL250005042751 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 862) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/862 `/scratch/stefan/7921153/working/3D/862' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O) `REAL250005042751.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042751.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042751/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042751 none COCCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 405 conformations in input total number of sets (complete confs): 405 using faster count positions algorithm for large data unique positions, atoms: [135, 135, 123, 53, 53, 53, 26, 26, 26, 26, 9, 1, 9, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 135, 135, 135, 135, 135, 123, 123, 53, 26, 26, 1, 26, 26, 78] 405 rigid atoms, others: [33, 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, 34, 35, 36]) total number of confs: 579 number of broken/clashed sets: 30 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042751 none COCCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 405 conformations in input total number of sets (complete confs): 405 using faster count positions algorithm for large data unique positions, atoms: [81, 57, 35, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 26, 26, 26, 26, 26, 1, 1, 1, 1, 81, 81, 81, 57, 57, 35, 35, 5, 1, 1, 26, 1, 1, 6] 405 rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 33, 36]) total number of confs: 324 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042751 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042751 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042751/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042751 Building REAL250005042752 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042752' /scratch/stefan/7921153/working/building/REAL250005042752 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042752 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042752/0 /scratch/stefan/7921153/working/building/REAL250005042752 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 863) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/863 `/scratch/stefan/7921153/working/3D/863' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O) `REAL250005042752.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042752.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042752/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042752 none CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [24, 24, 24, 18, 18, 19, 18, 7, 1, 7, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 24, 24, 24, 24, 18, 18, 1, 19, 19, 57] 72 rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29]) total number of confs: 118 number of broken/clashed sets: 13 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042752 none CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [6, 6, 6, 1, 1, 1, 1, 1, 1, 5, 5, 18, 18, 18, 19, 19, 1, 1, 1, 1, 6, 6, 6, 6, 1, 1, 18, 1, 1, 6] 72 rigid atoms, others: [3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 24, 25, 27, 28] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 26, 29]) total number of confs: 48 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042752 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042752 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042752/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042752 Building REAL250005042753 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042753' /scratch/stefan/7921153/working/building/REAL250005042753 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042753 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042753/0 /scratch/stefan/7921153/working/building/REAL250005042753 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 864) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/864 `/scratch/stefan/7921153/working/3D/864' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O)C1CC1) `REAL250005042753.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042753.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042753/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042753 none O=C(N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O)C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 5, 5, 5, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 243 conformations in input total number of sets (complete confs): 243 using faster count positions algorithm for large data unique positions, atoms: [13, 1, 13, 13, 43, 43, 43, 43, 67, 67, 81, 81, 81, 81, 81, 43, 43, 43, 43, 1, 1, 1, 13, 43, 43, 81, 43, 43, 129, 1, 1, 1, 1, 1] 243 rigid atoms, others: [32, 1, 33, 19, 20, 21, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 351 number of broken/clashed sets: 37 ./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: REAL250005042753 none O=C(N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O)C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 5, 5, 5, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 243 conformations in input total number of sets (complete confs): 243 using faster count positions algorithm for large data unique positions, atoms: [48, 48, 28, 28, 28, 27, 9, 1, 9, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 48, 81, 81, 48, 27, 27, 1, 28, 28, 84, 81, 81, 81, 81, 81] 243 rigid atoms, others: [7, 9, 10, 11, 12, 13, 14, 25] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 303 number of broken/clashed sets: 37 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042753 none O=C(N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O)C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 5, 5, 5, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 243 conformations in input total number of sets (complete confs): 243 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 27, 27, 27, 27, 27, 1, 1, 1, 1, 6, 43, 43, 6, 1, 1, 28, 1, 1, 3, 43, 43, 43, 43, 43] 243 rigid atoms, others: [2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 23, 24, 26, 27] set([0, 1, 33, 32, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 25, 28, 29, 30, 31]) total number of confs: 141 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042753 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042753 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042753/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042753 Building REAL250005042754 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042754' /scratch/stefan/7921153/working/building/REAL250005042754 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042754 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042754/0 /scratch/stefan/7921153/working/building/REAL250005042754 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 865) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/865 `/scratch/stefan/7921153/working/3D/865' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O)C1CCC1) `REAL250005042754.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042754/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042754 none O=C(N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O)C1CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 264 conformations in input total number of sets (complete confs): 264 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 31, 31, 31, 31, 76, 76, 88, 88, 88, 88, 88, 31, 31, 31, 31, 1, 1, 1, 1, 11, 31, 31, 88, 31, 31, 93, 1, 1, 1, 1, 1, 1, 1] 264 rigid atoms, others: [32, 1, 34, 35, 36, 33, 19, 20, 21, 22, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 335 number of broken/clashed sets: 14 ./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: REAL250005042754 none O=C(N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O)C1CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 264 conformations in input total number of sets (complete confs): 264 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 28, 28, 28, 28, 8, 1, 8, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 50, 88, 88, 88, 50, 28, 28, 1, 28, 28, 84, 88, 88, 88, 88, 88, 88, 88] 264 rigid atoms, others: [7, 9, 10, 11, 12, 13, 14, 26] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 327 number of broken/clashed sets: 14 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042754 none O=C(N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O)C1CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 264 conformations in input total number of sets (complete confs): 264 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 28, 28, 28, 28, 28, 1, 1, 1, 1, 5, 31, 31, 31, 5, 1, 1, 28, 1, 1, 3, 31, 31, 31, 31, 31, 31, 31] 264 rigid atoms, others: [2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 24, 25, 27, 28] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 26, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 115 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042754 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042754 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042754/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042754 Building REAL250005042755 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042755' /scratch/stefan/7921153/working/building/REAL250005042755 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042755 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042755/0 /scratch/stefan/7921153/working/building/REAL250005042755 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 866) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/866 `/scratch/stefan/7921153/working/3D/866' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1CC1)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O) `REAL250005042755.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042755.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042755/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042755 none O=C(CC1CC1)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 345 conformations in input total number of sets (complete confs): 345 using faster count positions algorithm for large data unique positions, atoms: [48, 48, 48, 96, 115, 115, 20, 20, 20, 20, 6, 1, 6, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 96, 96, 115, 115, 115, 115, 115, 48, 20, 20, 1, 20, 20, 60] 345 rigid atoms, others: [33, 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, 34, 35, 36]) total number of confs: 476 number of broken/clashed sets: 16 ./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: REAL250005042755 none O=C(CC1CC1)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 345 conformations in input total number of sets (complete confs): 345 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 39, 60, 60, 1, 1, 1, 1, 1, 1, 7, 7, 20, 20, 20, 20, 20, 1, 1, 1, 1, 39, 39, 60, 60, 60, 60, 60, 5, 1, 1, 20, 1, 1, 6] 345 rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 33, 36]) total number of confs: 246 number of broken/clashed sets: 16 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042755 none O=C(CC1CC1)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 345 conformations in input total number of sets (complete confs): 345 using faster count positions algorithm for large data unique positions, atoms: [24, 3, 1, 1, 1, 1, 24, 24, 60, 60, 60, 60, 107, 107, 115, 115, 115, 115, 115, 60, 60, 60, 60, 3, 3, 1, 1, 1, 1, 1, 24, 60, 60, 115, 60, 60, 180] 345 rigid atoms, others: [2, 3, 4, 5, 25, 26, 27, 28, 29] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 508 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042755 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042755 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042755/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042755 Building REAL250005042756 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042756' /scratch/stefan/7921153/working/building/REAL250005042756 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042756 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042756/0 /scratch/stefan/7921153/working/building/REAL250005042756 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 867) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/867 `/scratch/stefan/7921153/working/3D/867' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O) `REAL250005042756.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042756/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042756 none COCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 258 conformations in input total number of sets (complete confs): 258 using faster count positions algorithm for large data unique positions, atoms: [86, 86, 55, 55, 55, 25, 25, 25, 24, 8, 1, 8, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 86, 86, 86, 86, 86, 55, 24, 24, 1, 25, 25, 75] 258 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33]) total number of confs: 367 number of broken/clashed sets: 28 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042756 none COCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 258 conformations in input total number of sets (complete confs): 258 using faster count positions algorithm for large data unique positions, atoms: [44, 32, 5, 5, 5, 1, 1, 1, 1, 1, 1, 6, 6, 24, 24, 24, 24, 24, 1, 1, 1, 1, 44, 44, 44, 32, 32, 5, 1, 1, 24, 1, 1, 3] 258 rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 28, 29, 31] set([0, 1, 2, 3, 4, 33, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 30]) total number of confs: 164 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042756 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042756 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042756/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042756 Building REAL250005042757 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042757' /scratch/stefan/7921153/working/building/REAL250005042757 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042757 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042757/0 /scratch/stefan/7921153/working/building/REAL250005042757 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 868) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/868 `/scratch/stefan/7921153/working/3D/868' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O) `REAL250005042757.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042757/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042757 none CCCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 330 conformations in input total number of sets (complete confs): 330 using faster count positions algorithm for large data unique positions, atoms: [110, 106, 52, 52, 52, 22, 22, 22, 22, 6, 1, 6, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 110, 110, 110, 110, 110, 106, 106, 52, 22, 22, 1, 22, 22, 66] 330 rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35]) total number of confs: 471 number of broken/clashed sets: 21 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042757 none CCCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 330 conformations in input total number of sets (complete confs): 330 using faster count positions algorithm for large data unique positions, atoms: [44, 33, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 22, 22, 22, 22, 22, 1, 1, 1, 1, 51, 51, 51, 51, 51, 33, 33, 5, 1, 1, 22, 1, 1, 6] 330 rigid atoms, others: [33, 34, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 32, 35]) total number of confs: 291 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042757 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042757 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042757/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042757 Building REAL250005042758 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042758' /scratch/stefan/7921153/working/building/REAL250005042758 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042758 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042758/0 /scratch/stefan/7921153/working/building/REAL250005042758 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 869) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/869 `/scratch/stefan/7921153/working/3D/869' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O) `REAL250005042758.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042758/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042758 none CC(C)CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 228 conformations in input total number of sets (complete confs): 228 using faster count positions algorithm for large data unique positions, atoms: [74, 75, 76, 45, 45, 45, 18, 18, 18, 18, 5, 1, 5, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 76, 76, 76, 76, 76, 76, 76, 75, 75, 45, 18, 18, 1, 18, 18, 54] 228 rigid atoms, others: [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, 34, 36, 37, 38]) total number of confs: 326 number of broken/clashed sets: 18 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042758 none CC(C)CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 228 conformations in input total number of sets (complete confs): 228 using faster count positions algorithm for large data unique positions, atoms: [22, 20, 26, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 18, 18, 18, 18, 18, 1, 1, 1, 1, 26, 26, 26, 26, 26, 26, 26, 20, 20, 5, 1, 1, 18, 1, 1, 6] 228 rigid atoms, others: [33, 34, 36, 37, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 38]) total number of confs: 164 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042758 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042758 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042758/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042758 Building REAL250005042759 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042759' /scratch/stefan/7921153/working/building/REAL250005042759 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042759 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042759/0 /scratch/stefan/7921153/working/building/REAL250005042759 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 870) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/870 `/scratch/stefan/7921153/working/3D/870' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O) `REAL250005042759.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042759.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042759/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042759 none CC1CC1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 228 conformations in input total number of sets (complete confs): 228 using faster count positions algorithm for large data unique positions, atoms: [76, 76, 76, 51, 51, 51, 26, 26, 26, 26, 8, 1, 8, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 76, 76, 76, 76, 76, 76, 76, 51, 26, 26, 1, 26, 26, 78] 228 rigid atoms, others: [33, 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, 34, 35, 36]) total number of confs: 290 number of broken/clashed sets: 28 ./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: REAL250005042759 none CC1CC1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 228 conformations in input total number of sets (complete confs): 228 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 28, 5, 5, 5, 1, 1, 1, 1, 1, 1, 6, 6, 26, 26, 26, 26, 26, 1, 1, 1, 1, 28, 28, 28, 28, 28, 28, 28, 5, 1, 1, 26, 1, 1, 3] 228 rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 33, 36]) total number of confs: 105 number of broken/clashed sets: 28 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042759 none CC1CC1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 228 conformations in input total number of sets (complete confs): 228 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 10, 10, 10, 28, 28, 28, 28, 61, 61, 76, 76, 76, 76, 76, 28, 28, 28, 28, 2, 2, 2, 1, 1, 1, 1, 10, 28, 28, 76, 28, 28, 84] 228 rigid atoms, others: [0, 1, 2, 3, 4, 26, 27, 28, 29] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 293 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042759 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042759 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042759/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042759 Building REAL250005042760 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042760' /scratch/stefan/7921153/working/building/REAL250005042760 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042760 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042760/0 /scratch/stefan/7921153/working/building/REAL250005042760 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 871) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/871 `/scratch/stefan/7921153/working/3D/871' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O) `REAL250005042760.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042760/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042760 none CCOCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 438 conformations in input total number of sets (complete confs): 438 using faster count positions algorithm for large data unique positions, atoms: [146, 146, 140, 66, 66, 66, 30, 29, 30, 29, 9, 1, 9, 1, 1, 1, 1, 1, 1, 29, 30, 30, 30, 146, 146, 146, 146, 146, 140, 140, 66, 29, 29, 1, 29, 29, 90] 438 rigid atoms, others: [33, 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, 34, 35, 36]) total number of confs: 600 number of broken/clashed sets: 45 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042760 none CCOCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 438 conformations in input total number of sets (complete confs): 438 using faster count positions algorithm for large data unique positions, atoms: [83, 76, 41, 5, 5, 5, 1, 1, 1, 1, 1, 1, 6, 6, 29, 29, 29, 29, 29, 1, 1, 1, 1, 83, 83, 83, 83, 83, 41, 41, 5, 1, 1, 29, 1, 1, 3] 438 rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 33, 36]) total number of confs: 271 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042760 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042760 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042760/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042760 Building REAL250005042761 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042761' /scratch/stefan/7921153/working/building/REAL250005042761 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042761 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042761/0 /scratch/stefan/7921153/working/building/REAL250005042761 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 872) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/872 `/scratch/stefan/7921153/working/3D/872' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)=CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O) `REAL250005042761.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042761/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042761 none CC(C)=CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 5, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [63, 63, 63, 43, 43, 43, 20, 20, 20, 19, 9, 1, 9, 1, 1, 1, 1, 1, 1, 19, 20, 20, 20, 63, 63, 63, 63, 63, 63, 63, 43, 19, 19, 1, 19, 20, 60] 189 rigid atoms, others: [33, 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, 34, 35, 36]) total number of confs: 253 number of broken/clashed sets: 31 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042761 none CC(C)=CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 5, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [25, 25, 25, 6, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 19, 19, 19, 19, 19, 1, 1, 1, 1, 25, 25, 25, 25, 25, 25, 25, 6, 1, 1, 19, 1, 1, 6] 189 rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 33, 36]) total number of confs: 96 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042761 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042761 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042761/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042761 Building REAL250005042762 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042762' /scratch/stefan/7921153/working/building/REAL250005042762 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042762 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042762/0 /scratch/stefan/7921153/working/building/REAL250005042762 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 873) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/873 `/scratch/stefan/7921153/working/3D/873' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O) `REAL250005042762.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042762/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042762 none CCCCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 426 conformations in input total number of sets (complete confs): 426 using faster count positions algorithm for large data unique positions, atoms: [141, 139, 129, 53, 53, 53, 21, 21, 21, 21, 7, 1, 7, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 141, 142, 142, 142, 142, 140, 140, 129, 129, 53, 21, 21, 1, 21, 21, 63] 426 rigid atoms, others: [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, 34, 36, 37, 38]) total number of confs: 601 number of broken/clashed sets: 38 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042762 none CCCCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 426 conformations in input total number of sets (complete confs): 426 using faster count positions algorithm for large data unique positions, atoms: [76, 50, 33, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 21, 21, 21, 21, 21, 1, 1, 1, 1, 76, 79, 79, 77, 76, 61, 61, 33, 33, 5, 1, 1, 21, 1, 1, 6] 426 rigid atoms, others: [33, 34, 36, 37, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 38]) total number of confs: 455 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042762 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042762 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042762/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042762 Building REAL250005042763 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042763' /scratch/stefan/7921153/working/building/REAL250005042763 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042763 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042763/0 /scratch/stefan/7921153/working/building/REAL250005042763 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 874) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/874 `/scratch/stefan/7921153/working/3D/874' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O) `REAL250005042763.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042763.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042763/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042763 none CC(C)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [57, 38, 57, 38, 38, 21, 21, 21, 21, 6, 1, 6, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 57, 57, 57, 57, 57, 57, 57, 38, 21, 21, 1, 21, 21, 63] 171 rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35]) total number of confs: 254 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042763 none CC(C)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [24, 5, 24, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 21, 21, 21, 21, 21, 1, 1, 1, 1, 24, 24, 24, 24, 24, 24, 24, 5, 1, 1, 21, 1, 1, 6] 171 rigid atoms, others: [33, 34, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 32, 35]) total number of confs: 119 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042763 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042763 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042763/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042763 Building REAL250005042764 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042764' /scratch/stefan/7921153/working/building/REAL250005042764 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042764 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042764/0 /scratch/stefan/7921153/working/building/REAL250005042764 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 875) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/875 `/scratch/stefan/7921153/working/3D/875' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O) `REAL250005042764.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042764/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042764 none CCC(C)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 372 conformations in input total number of sets (complete confs): 372 using faster count positions algorithm for large data unique positions, atoms: [124, 121, 60, 121, 60, 60, 25, 24, 25, 24, 9, 1, 9, 1, 1, 1, 1, 1, 1, 24, 25, 25, 25, 124, 124, 124, 124, 124, 121, 121, 121, 121, 60, 24, 24, 1, 24, 24, 74] 372 rigid atoms, others: [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, 34, 36, 37, 38]) total number of confs: 533 number of broken/clashed sets: 66 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042764 none CCC(C)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 372 conformations in input total number of sets (complete confs): 372 using faster count positions algorithm for large data unique positions, atoms: [53, 43, 6, 43, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 24, 24, 24, 24, 24, 1, 1, 1, 1, 59, 59, 59, 59, 59, 43, 43, 43, 43, 6, 1, 1, 24, 1, 1, 3] 372 rigid atoms, others: [33, 34, 36, 37, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 38]) total number of confs: 310 number of broken/clashed sets: 66 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042764 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042764 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042764/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042764 Building REAL250005042765 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042765' /scratch/stefan/7921153/working/building/REAL250005042765 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042765 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042765/0 /scratch/stefan/7921153/working/building/REAL250005042765 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 876) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/876 `/scratch/stefan/7921153/working/3D/876' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O) `REAL250005042765.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042765.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042765/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042765 none COC(C)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [50, 50, 35, 50, 35, 35, 18, 18, 18, 17, 6, 1, 6, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 50, 50, 50, 50, 50, 50, 50, 35, 17, 17, 1, 18, 18, 54] 150 rigid atoms, others: [33, 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, 34, 35, 36]) total number of confs: 216 number of broken/clashed sets: 26 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042765 none COC(C)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [32, 26, 6, 26, 6, 6, 1, 1, 1, 1, 1, 1, 5, 5, 17, 17, 17, 17, 17, 1, 1, 1, 1, 32, 32, 32, 26, 26, 26, 26, 6, 1, 1, 18, 1, 1, 3] 150 rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 33, 36]) total number of confs: 131 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042765 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042765 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042765/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042765 Building REAL250005042766 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042766' /scratch/stefan/7921153/working/building/REAL250005042766 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042766 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042766/0 /scratch/stefan/7921153/working/building/REAL250005042766 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 877) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/877 `/scratch/stefan/7921153/working/3D/877' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O) `REAL250005042766.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042766.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042766/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042766 none C=CCCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 179, 72, 72, 72, 26, 25, 25, 25, 8, 1, 8, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 201, 201, 201, 201, 201, 179, 179, 72, 25, 25, 1, 25, 25, 76] 603 rigid atoms, others: [33, 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, 34, 35, 36]) total number of confs: 838 number of broken/clashed sets: 112 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042766 none C=CCCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [132, 82, 44, 6, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 25, 25, 26, 25, 25, 1, 1, 1, 1, 132, 132, 132, 82, 82, 44, 44, 6, 1, 1, 25, 1, 1, 3] 603 rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 33, 36]) total number of confs: 572 number of broken/clashed sets: 112 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042766 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042766 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042766/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042766 Building REAL250005042767 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042767' /scratch/stefan/7921153/working/building/REAL250005042767 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042767 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042767/0 /scratch/stefan/7921153/working/building/REAL250005042767 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 878) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/878 `/scratch/stefan/7921153/working/3D/878' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=C(C)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O) `REAL250005042767.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042767.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042767/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042767 none CC=C(C)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 252 conformations in input total number of sets (complete confs): 252 using faster count positions algorithm for large data unique positions, atoms: [84, 84, 47, 84, 47, 47, 26, 26, 26, 25, 8, 1, 8, 1, 1, 1, 1, 1, 1, 25, 25, 26, 26, 84, 84, 84, 84, 84, 84, 84, 47, 25, 25, 1, 25, 25, 78] 252 rigid atoms, others: [33, 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, 34, 35, 36]) total number of confs: 305 number of broken/clashed sets: 49 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042767 none CC=C(C)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 252 conformations in input total number of sets (complete confs): 252 using faster count positions algorithm for large data unique positions, atoms: [36, 36, 6, 36, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 25, 25, 25, 25, 25, 1, 1, 1, 1, 36, 36, 36, 36, 36, 36, 36, 6, 1, 1, 25, 1, 1, 3] 252 rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 33, 36]) total number of confs: 123 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042767 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042767 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042767/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042767 Building REAL250005042768 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042768' /scratch/stefan/7921153/working/building/REAL250005042768 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042768 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042768/0 /scratch/stefan/7921153/working/building/REAL250005042768 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 879) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/879 `/scratch/stefan/7921153/working/3D/879' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C(=O)N[C@@H]2CN(C(=O)C3=CC(=O)[N-]O3)C[C@@H]2O)CC1) `REAL250005042768.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042768.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042768/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042768 none CC1(C(=O)N[C@@H]2CN(C(=O)C3=CC(=O)[N-]O3)C[C@@H]2O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [64, 39, 39, 39, 21, 22, 22, 21, 6, 1, 6, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 64, 64, 64, 64, 64, 39, 21, 21, 1, 22, 22, 66, 64, 64, 64, 64] 192 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 258 number of broken/clashed sets: 26 ./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: REAL250005042768 none CC1(C(=O)N[C@@H]2CN(C(=O)C3=CC(=O)[N-]O3)C[C@@H]2O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [26, 6, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 21, 22, 22, 22, 22, 1, 1, 1, 1, 26, 26, 26, 26, 26, 6, 1, 1, 21, 1, 1, 3, 26, 26, 26, 26] 192 rigid atoms, others: [4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 27, 28, 30, 31] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 29, 32, 33, 34, 35, 36]) total number of confs: 100 number of broken/clashed sets: 26 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042768 none CC1(C(=O)N[C@@H]2CN(C(=O)C3=CC(=O)[N-]O3)C[C@@H]2O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 192 conformations in input total number of sets (complete confs): 192 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 7, 7, 7, 26, 26, 26, 26, 60, 60, 64, 64, 64, 64, 64, 26, 26, 26, 26, 1, 1, 2, 2, 2, 7, 26, 26, 64, 26, 26, 78, 1, 1, 1, 1] 192 rigid atoms, others: [0, 1, 2, 35, 36, 33, 34, 21, 22] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 261 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042768 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042768 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042768/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042768 Building REAL250005042769 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042769' /scratch/stefan/7921153/working/building/REAL250005042769 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042769 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042769/0 /scratch/stefan/7921153/working/building/REAL250005042769 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 880) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/880 `/scratch/stefan/7921153/working/3D/880' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H]1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O) `REAL250005042769.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042769.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042769/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042769 none C[C@@H]1C[C@H]1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 288 conformations in input total number of sets (complete confs): 288 using faster count positions algorithm for large data unique positions, atoms: [96, 96, 96, 96, 56, 96, 56, 56, 28, 28, 28, 28, 10, 1, 10, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 96, 96, 96, 96, 96, 56, 28, 28, 1, 28, 28, 84] 288 rigid atoms, others: [33, 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, 34, 35, 36]) total number of confs: 356 number of broken/clashed sets: 43 ./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: REAL250005042769 none C[C@@H]1C[C@H]1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 288 conformations in input total number of sets (complete confs): 288 using faster count positions algorithm for large data unique positions, atoms: [41, 41, 41, 41, 6, 41, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 28, 28, 28, 28, 28, 1, 1, 1, 1, 41, 41, 41, 41, 41, 6, 1, 1, 28, 1, 1, 3] 288 rigid atoms, others: [32, 34, 35, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 33, 36]) total number of confs: 136 number of broken/clashed sets: 43 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042769 none C[C@@H]1C[C@H]1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 288 conformations in input total number of sets (complete confs): 288 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 41, 41, 41, 41, 77, 77, 96, 96, 96, 96, 96, 41, 41, 41, 41, 2, 2, 2, 1, 1, 13, 41, 41, 96, 41, 41, 123] 288 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 389 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042769 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042769 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042769/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042769 Building REAL250005042770 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042770' /scratch/stefan/7921153/working/building/REAL250005042770 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042770 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042770/0 /scratch/stefan/7921153/working/building/REAL250005042770 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 881) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/881 `/scratch/stefan/7921153/working/3D/881' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@@H]1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O) `REAL250005042770.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042770/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042770 none C[C@H]1C[C@@H]1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [64, 64, 64, 64, 35, 64, 35, 35, 16, 15, 15, 15, 5, 1, 5, 1, 1, 1, 1, 1, 1, 15, 15, 16, 16, 64, 64, 64, 64, 64, 35, 15, 15, 1, 15, 15, 48] 192 rigid atoms, others: [33, 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, 34, 35, 36]) total number of confs: 225 number of broken/clashed sets: 29 ./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: REAL250005042770 none C[C@H]1C[C@@H]1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [34, 34, 34, 34, 6, 34, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 15, 15, 15, 15, 15, 1, 1, 1, 1, 34, 34, 34, 34, 34, 6, 1, 1, 15, 1, 1, 3] 192 rigid atoms, others: [32, 34, 35, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 33, 36]) total number of confs: 108 number of broken/clashed sets: 29 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042770 none C[C@H]1C[C@@H]1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 192 conformations in input total number of sets (complete confs): 192 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 34, 34, 34, 34, 64, 64, 64, 64, 64, 64, 64, 34, 34, 34, 34, 2, 2, 2, 1, 1, 11, 34, 34, 64, 34, 34, 102] 192 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 301 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042770 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042770 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042770/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042770 Building REAL250005042771 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042771' /scratch/stefan/7921153/working/building/REAL250005042771 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042771 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042771/0 /scratch/stefan/7921153/working/building/REAL250005042771 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 882) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/882 `/scratch/stefan/7921153/working/3D/882' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O) `REAL250005042771.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042771.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042771/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042771 none NC(=O)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 6, 6, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [30, 27, 30, 27, 27, 13, 13, 14, 13, 6, 1, 6, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 30, 30, 27, 13, 13, 1, 14, 14, 42] 90 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30]) total number of confs: 125 number of broken/clashed sets: 14 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042771 none NC(=O)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 6, 6, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [15, 6, 15, 6, 6, 1, 1, 1, 1, 1, 1, 4, 4, 13, 14, 14, 14, 14, 1, 1, 1, 1, 15, 15, 6, 1, 1, 13, 1, 1, 3] 90 rigid atoms, others: [5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 25, 26, 28, 29] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 27, 30]) total number of confs: 67 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042771 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042771 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042771/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042771 Building REAL250005042772 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042772' /scratch/stefan/7921153/working/building/REAL250005042772 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042772 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042772/0 /scratch/stefan/7921153/working/building/REAL250005042772 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 883) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/883 `/scratch/stefan/7921153/working/3D/883' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O) `REAL250005042772.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042772/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042772 none CC(C)(C)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [35, 32, 35, 35, 32, 32, 17, 17, 18, 17, 7, 1, 7, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 35, 35, 35, 35, 35, 35, 35, 35, 35, 32, 17, 17, 1, 18, 18, 54] 105 rigid atoms, others: [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, 34, 36, 37, 38]) total number of confs: 160 number of broken/clashed sets: 17 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042772 none CC(C)(C)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [12, 6, 12, 12, 6, 6, 1, 1, 1, 1, 1, 1, 5, 5, 17, 17, 17, 18, 18, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 1, 1, 17, 1, 1, 6] 105 rigid atoms, others: [33, 34, 36, 37, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 38]) total number of confs: 77 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042772 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042772 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042772/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042772 Building REAL250005042773 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042773' /scratch/stefan/7921153/working/building/REAL250005042773 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042773 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042773/0 /scratch/stefan/7921153/working/building/REAL250005042773 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 884) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/884 `/scratch/stefan/7921153/working/3D/884' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O) `REAL250005042773.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042773.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042773/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042773 none C=CCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 261 conformations in input total number of sets (complete confs): 261 using faster count positions algorithm for large data unique positions, atoms: [87, 87, 49, 49, 49, 25, 25, 25, 24, 9, 1, 9, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 87, 87, 87, 87, 87, 49, 24, 24, 1, 25, 25, 75] 261 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33]) total number of confs: 386 number of broken/clashed sets: 26 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042773 none C=CCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 261 conformations in input total number of sets (complete confs): 261 using faster count positions algorithm for large data unique positions, atoms: [53, 30, 5, 5, 5, 1, 1, 1, 1, 1, 1, 6, 6, 24, 24, 24, 24, 24, 1, 1, 1, 1, 53, 53, 53, 30, 30, 5, 1, 1, 25, 1, 1, 3] 261 rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 28, 29, 31] set([0, 1, 2, 3, 4, 33, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 30]) total number of confs: 220 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042773 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042773 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042773/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042773 Building REAL250005042774 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042774' /scratch/stefan/7921153/working/building/REAL250005042774 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005042774 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042774/0 /scratch/stefan/7921153/working/building/REAL250005042774 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 885) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/885 `/scratch/stefan/7921153/working/3D/885' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[NH+](C)CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O) `REAL250005042774.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042774/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042774 none C[NH+](C)CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 1, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [15, 15, 15, 15, 15, 15, 15, 11, 11, 11, 11, 5, 1, 5, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 15, 15, 15, 15, 15, 15, 15, 15, 15, 11, 11, 1, 11, 11, 33] 45 rigid atoms, others: [35, 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, 36, 37, 38]) total number of confs: 67 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042774 none C[NH+](C)CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 1, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [10, 8, 10, 10, 4, 4, 4, 1, 1, 1, 1, 1, 1, 5, 5, 11, 11, 11, 11, 11, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 8, 8, 4, 1, 1, 11, 1, 1, 6] 45 rigid atoms, others: [33, 34, 36, 37, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 38]) total number of confs: 63 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042774 /scratch/stefan/7921153/working /scratch/stefan/7921153 mkdir: created directory `1' /scratch/stefan/7921153/working/building/REAL250005042774/1 /scratch/stefan/7921153/working/building/REAL250005042774 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 1 (index: 886) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/886 `/scratch/stefan/7921153/working/3D/886' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O) `REAL250005042774.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005042774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042774/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042774 none CN(C)CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 186 conformations in input total number of sets (complete confs): 186 using faster count positions algorithm for large data unique positions, atoms: [62, 60, 62, 34, 34, 34, 19, 19, 19, 19, 7, 1, 7, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 62, 62, 62, 62, 62, 62, 60, 60, 34, 19, 19, 1, 19, 19, 57] 186 rigid atoms, others: [34, 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, 35, 36, 37]) total number of confs: 265 number of broken/clashed sets: 13 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042774 none CN(C)CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 186 conformations in input total number of sets (complete confs): 186 using faster count positions algorithm for large data unique positions, atoms: [33, 26, 33, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 19, 19, 19, 19, 19, 1, 1, 1, 1, 33, 33, 33, 33, 33, 33, 26, 26, 5, 1, 1, 19, 1, 1, 6] 186 rigid atoms, others: [32, 33, 35, 36, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 37]) total number of confs: 149 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042774 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042774 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 1: /scratch/stefan/7921153/working/building/REAL250005042774/1.* 0: /scratch/stefan/7921153/working/building/REAL250005042774/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042774 Building REAL250005042775 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042775' /scratch/stefan/7921153/working/building/REAL250005042775 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042775 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042775/0 /scratch/stefan/7921153/working/building/REAL250005042775 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 887) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/887 `/scratch/stefan/7921153/working/3D/887' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(O)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O) `REAL250005042775.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042775.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042775/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:2-3 Rotatable hydrogens reported. Reducing confs by a factor of 3 WARNING:root:Setting energy window to 12 and max confs to 66 ('energy: ', 12.0) ('conf: ', 66) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042775 none C=CC(O)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [67, 67, 36, 67, 36, 36, 13, 14, 14, 13, 5, 1, 5, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 67, 67, 67, 67, 201, 36, 13, 13, 1, 14, 14, 42] 603 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 31] 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, 32, 33, 34]) total number of confs: 478 number of broken/clashed sets: 105 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042775 none C=CC(O)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [47, 33, 6, 33, 6, 6, 1, 1, 1, 1, 1, 1, 5, 5, 13, 14, 14, 14, 14, 1, 1, 1, 1, 47, 47, 47, 33, 99, 6, 1, 1, 13, 1, 1, 3] 603 rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 29, 30] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 34, 23, 24, 25, 26, 27, 28, 31]) total number of confs: 280 number of broken/clashed sets: 105 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042775 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042775 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042775/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042775 Building REAL250005042776 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042776' /scratch/stefan/7921153/working/building/REAL250005042776 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042776 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042776/0 /scratch/stefan/7921153/working/building/REAL250005042776 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 888) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/888 `/scratch/stefan/7921153/working/3D/888' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O)C1COC1) `REAL250005042776.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042776.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042776/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042776 none O=C(N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O)C1COC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 5, 5, 12, 5, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 255 conformations in input total number of sets (complete confs): 255 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 31, 31, 31, 31, 76, 76, 85, 85, 85, 85, 85, 31, 31, 31, 31, 1, 1, 1, 1, 12, 31, 31, 85, 31, 31, 93, 1, 1, 1, 1, 1] 255 rigid atoms, others: [32, 1, 34, 33, 19, 20, 21, 22, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 327 number of broken/clashed sets: 24 ./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: REAL250005042776 none O=C(N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O)C1COC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 5, 5, 12, 5, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 255 conformations in input total number of sets (complete confs): 255 using faster count positions algorithm for large data unique positions, atoms: [60, 60, 27, 27, 27, 26, 8, 1, 8, 1, 1, 1, 1, 1, 1, 26, 27, 27, 27, 60, 85, 85, 85, 60, 26, 26, 1, 26, 26, 81, 85, 85, 85, 85, 85] 255 rigid atoms, others: [7, 9, 10, 11, 12, 13, 14, 26] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 315 number of broken/clashed sets: 24 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042776 none O=C(N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O)C1COC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 5, 5, 12, 5, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 255 conformations in input total number of sets (complete confs): 255 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 1, 1, 1, 1, 1, 1, 6, 6, 26, 26, 26, 26, 26, 1, 1, 1, 1, 5, 31, 31, 31, 5, 1, 1, 26, 1, 1, 3, 31, 31, 31, 31, 31] 255 rigid atoms, others: [2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 24, 25, 27, 28] set([0, 1, 34, 33, 32, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 26, 29, 30, 31]) total number of confs: 112 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042776 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042776 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042776/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042776 Building REAL250005042777 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042777' /scratch/stefan/7921153/working/building/REAL250005042777 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042777 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042777/0 /scratch/stefan/7921153/working/building/REAL250005042777 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 889) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/889 `/scratch/stefan/7921153/working/3D/889' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H](C)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O) `REAL250005042777.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042777.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042777/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042777 none CO[C@H](C)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 165 conformations in input total number of sets (complete confs): 165 using faster count positions algorithm for large data unique positions, atoms: [55, 55, 36, 55, 55, 36, 36, 18, 18, 18, 17, 6, 1, 6, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 55, 55, 55, 55, 55, 55, 36, 17, 17, 1, 18, 18, 54] 165 rigid atoms, others: [33, 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, 34, 35, 36]) total number of confs: 230 number of broken/clashed sets: 25 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042777 none CO[C@H](C)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 165 conformations in input total number of sets (complete confs): 165 using faster count positions algorithm for large data unique positions, atoms: [40, 34, 6, 34, 34, 6, 6, 1, 1, 1, 1, 1, 1, 5, 5, 17, 17, 17, 17, 17, 1, 1, 1, 1, 40, 40, 40, 34, 34, 34, 6, 1, 1, 18, 1, 1, 3] 165 rigid atoms, others: [32, 34, 35, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 33, 36]) total number of confs: 156 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042777 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042777 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042777/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042777 Building REAL250005042778 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042778' /scratch/stefan/7921153/working/building/REAL250005042778 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042778 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042778/0 /scratch/stefan/7921153/working/building/REAL250005042778 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 890) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/890 `/scratch/stefan/7921153/working/3D/890' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC=CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O) `REAL250005042778.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042778.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042778/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042778 none CCC=CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 267 conformations in input total number of sets (complete confs): 267 using faster count positions algorithm for large data unique positions, atoms: [89, 72, 72, 47, 47, 47, 20, 20, 20, 19, 7, 1, 7, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 89, 89, 89, 89, 89, 72, 72, 47, 19, 19, 1, 20, 20, 60] 267 rigid atoms, others: [33, 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, 34, 35, 36]) total number of confs: 364 number of broken/clashed sets: 42 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042778 none CCC=CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 267 conformations in input total number of sets (complete confs): 267 using faster count positions algorithm for large data unique positions, atoms: [53, 34, 34, 6, 6, 6, 1, 1, 1, 1, 1, 1, 5, 5, 19, 19, 19, 20, 20, 1, 1, 1, 1, 53, 53, 53, 53, 53, 34, 34, 6, 1, 1, 19, 1, 1, 6] 267 rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 33, 36]) total number of confs: 221 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042778 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042778 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042778/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042778 Building REAL250005042779 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042779' /scratch/stefan/7921153/working/building/REAL250005042779 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types Protomer extracton resulted in 0 protomers Marking REAL250005042779 as failed and skipping /scratch/stefan/7921153/working /scratch/stefan/7921153 `/scratch/stefan/7921153/working/building/REAL250005042779' -> `/scratch/stefan/7921153/failed/REAL250005042779' Building REAL250005042780 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042780' /scratch/stefan/7921153/working/building/REAL250005042780 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042780 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042780/0 /scratch/stefan/7921153/working/building/REAL250005042780 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 891) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/891 `/scratch/stefan/7921153/working/3D/891' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CO)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O) `REAL250005042780.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042780.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042780/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:2-3 Rotatable hydrogens reported. Reducing confs by a factor of 3 WARNING:root:Setting energy window to 12 and max confs to 66 ('energy: ', 12.0) ('conf: ', 66) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042780 none O=C(CO)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 7, 4, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 378 conformations in input total number of sets (complete confs): 378 using faster count positions algorithm for large data unique positions, atoms: [41, 41, 41, 42, 22, 21, 22, 21, 7, 1, 7, 1, 1, 1, 1, 1, 1, 21, 22, 22, 22, 42, 42, 126, 41, 21, 21, 1, 21, 21, 66] 378 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30]) total number of confs: 309 number of broken/clashed sets: 27 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042780 none O=C(CO)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 7, 4, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 378 conformations in input total number of sets (complete confs): 378 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 25, 1, 1, 1, 1, 1, 1, 6, 6, 21, 21, 21, 21, 21, 1, 1, 1, 1, 25, 25, 75, 5, 1, 1, 21, 1, 1, 3] 378 rigid atoms, others: [4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 25, 26, 28, 29] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 27, 30]) total number of confs: 193 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042780 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042780 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042780/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042780 Building REAL250005042781 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042781' /scratch/stefan/7921153/working/building/REAL250005042781 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042781 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042781/0 /scratch/stefan/7921153/working/building/REAL250005042781 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 892) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/892 `/scratch/stefan/7921153/working/3D/892' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O) `REAL250005042781.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042781/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:2-3 Rotatable hydrogens reported. Reducing confs by a factor of 3 WARNING:root:Setting energy window to 12 and max confs to 66 ('energy: ', 12.0) ('conf: ', 66) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042781 none CC(O)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 387 conformations in input total number of sets (complete confs): 387 using faster count positions algorithm for large data unique positions, atoms: [43, 32, 43, 32, 32, 17, 18, 18, 17, 6, 1, 6, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 43, 43, 43, 43, 129, 32, 17, 17, 1, 18, 18, 54] 387 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33]) total number of confs: 325 number of broken/clashed sets: 60 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042781 none CC(O)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 387 conformations in input total number of sets (complete confs): 387 using faster count positions algorithm for large data unique positions, atoms: [26, 6, 26, 6, 6, 1, 1, 1, 1, 1, 1, 5, 5, 17, 18, 18, 18, 18, 1, 1, 1, 1, 26, 26, 26, 26, 78, 6, 1, 1, 17, 1, 1, 3] 387 rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 28, 29, 31] set([0, 1, 2, 3, 4, 33, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 30]) total number of confs: 197 number of broken/clashed sets: 60 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042781 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042781 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042781/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042781 Building REAL250005042782 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042782' /scratch/stefan/7921153/working/building/REAL250005042782 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042782 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042782/0 /scratch/stefan/7921153/working/building/REAL250005042782 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 893) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/893 `/scratch/stefan/7921153/working/3D/893' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O)C1CC1F) `REAL250005042782.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042782.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042782/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042782 none O=C(N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O)C1CC1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 5, 5, 5, 15, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 273 conformations in input total number of sets (complete confs): 273 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 37, 37, 37, 37, 82, 82, 91, 91, 91, 91, 91, 37, 37, 37, 37, 1, 1, 1, 1, 12, 37, 37, 91, 37, 37, 111, 1, 1, 1, 1] 273 rigid atoms, others: [32, 1, 33, 19, 20, 21, 22, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 360 number of broken/clashed sets: 20 ./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: REAL250005042782 none O=C(N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O)C1CC1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 5, 5, 5, 15, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 273 conformations in input total number of sets (complete confs): 273 using faster count positions algorithm for large data unique positions, atoms: [54, 54, 27, 27, 27, 26, 9, 1, 9, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 54, 91, 91, 91, 54, 26, 26, 1, 27, 27, 81, 91, 91, 91, 91] 273 rigid atoms, others: [7, 9, 10, 11, 12, 13, 14, 26] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 340 number of broken/clashed sets: 20 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042782 none O=C(N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O)C1CC1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 5, 5, 5, 15, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 273 conformations in input total number of sets (complete confs): 273 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 1, 1, 1, 1, 1, 1, 6, 6, 26, 26, 26, 26, 26, 1, 1, 1, 1, 5, 37, 37, 37, 5, 1, 1, 27, 1, 1, 3, 37, 37, 37, 37] 273 rigid atoms, others: [2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 24, 25, 27, 28] set([0, 1, 33, 32, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 26, 29, 30, 31]) total number of confs: 126 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042782 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042782 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042782/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042782 Building REAL250005042783 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042783' /scratch/stefan/7921153/working/building/REAL250005042783 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042783 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042783/0 /scratch/stefan/7921153/working/building/REAL250005042783 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 894) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/894 `/scratch/stefan/7921153/working/3D/894' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCF)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O) `REAL250005042783.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042783.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042783/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042783 none O=C(CCF)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'F', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 15, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 315 conformations in input total number of sets (complete confs): 315 using faster count positions algorithm for large data unique positions, atoms: [56, 56, 56, 105, 105, 21, 21, 21, 21, 5, 1, 5, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 105, 105, 105, 105, 56, 21, 21, 1, 21, 21, 63] 315 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32]) total number of confs: 429 number of broken/clashed sets: 16 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042783 none O=C(CCF)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'F', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 15, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 315 conformations in input total number of sets (complete confs): 315 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 34, 53, 1, 1, 1, 1, 1, 1, 7, 7, 21, 21, 21, 21, 21, 1, 1, 1, 1, 34, 34, 53, 53, 5, 1, 1, 21, 1, 1, 6] 315 rigid atoms, others: [5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 27, 28, 30, 31] set([0, 1, 2, 3, 4, 32, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 29]) total number of confs: 261 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042783 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042783 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042783/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042783 Building REAL250005042784 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042784' /scratch/stefan/7921153/working/building/REAL250005042784 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042784 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042784/0 /scratch/stefan/7921153/working/building/REAL250005042784 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 895) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/895 `/scratch/stefan/7921153/working/3D/895' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(C=CCF)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O) `REAL250005042784.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042784/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042784 none O=C(C=CCF)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 1, 1, 5, 15, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 153 conformations in input total number of sets (complete confs): 153 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 32, 49, 49, 51, 13, 13, 13, 12, 6, 1, 6, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 49, 49, 51, 51, 32, 12, 12, 1, 13, 13, 39] 153 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33]) total number of confs: 191 number of broken/clashed sets: 26 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042784 none O=C(C=CCF)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 1, 1, 5, 15, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 153 conformations in input total number of sets (complete confs): 153 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 23, 23, 41, 1, 1, 1, 1, 1, 1, 5, 5, 12, 12, 12, 13, 13, 1, 1, 1, 1, 23, 23, 41, 41, 6, 1, 1, 12, 1, 1, 6] 153 rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 28, 29, 31] set([0, 1, 2, 3, 4, 5, 33, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 30]) total number of confs: 171 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042784 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042784 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042784/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042784 Building REAL250005042785 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042785' /scratch/stefan/7921153/working/building/REAL250005042785 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042785 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042785/0 /scratch/stefan/7921153/working/building/REAL250005042785 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 896) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/896 `/scratch/stefan/7921153/working/3D/896' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O) `REAL250005042785.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042785.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042785/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042785 none C#CCCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 399 conformations in input total number of sets (complete confs): 399 using faster count positions algorithm for large data unique positions, atoms: [133, 133, 120, 54, 54, 54, 23, 23, 23, 23, 6, 1, 6, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 133, 133, 133, 120, 120, 54, 23, 23, 1, 23, 23, 69] 399 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 31] 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, 32, 33, 34]) total number of confs: 572 number of broken/clashed sets: 25 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042785 none C#CCCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 399 conformations in input total number of sets (complete confs): 399 using faster count positions algorithm for large data unique positions, atoms: [59, 59, 35, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 23, 23, 23, 23, 23, 1, 1, 1, 1, 59, 59, 59, 35, 35, 5, 1, 1, 23, 1, 1, 6] 399 rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 29, 30] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 34, 23, 24, 25, 26, 27, 28, 31]) total number of confs: 289 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042785 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042785 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042785/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042785 Building REAL250005042786 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042786' /scratch/stefan/7921153/working/building/REAL250005042786 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042786 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042786/0 /scratch/stefan/7921153/working/building/REAL250005042786 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 897) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/897 `/scratch/stefan/7921153/working/3D/897' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O)C1CCO1) `REAL250005042786.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042786.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042786/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042786 none O=C(N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O)C1CCO1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 5, 5, 5, 12, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 96 conformations in input total number of sets (complete confs): 96 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 20, 20, 20, 20, 28, 28, 32, 32, 32, 32, 32, 20, 20, 20, 20, 1, 1, 1, 1, 8, 20, 20, 32, 20, 20, 60, 1, 1, 1, 1, 1] 96 rigid atoms, others: [32, 1, 34, 33, 19, 20, 21, 22, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 151 number of broken/clashed sets: 14 ./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: REAL250005042786 none O=C(N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O)C1CCO1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 5, 5, 5, 12, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 96 conformations in input total number of sets (complete confs): 96 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 18, 18, 18, 17, 7, 1, 7, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 25, 32, 32, 32, 25, 17, 17, 1, 18, 18, 54, 32, 32, 32, 32, 32] 96 rigid atoms, others: [7, 9, 10, 11, 12, 13, 14, 26] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 137 number of broken/clashed sets: 14 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042786 none O=C(N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O)C1CCO1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 5, 5, 5, 12, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 96 conformations in input total number of sets (complete confs): 96 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 1, 4, 4, 17, 17, 17, 17, 17, 1, 1, 1, 1, 6, 20, 20, 20, 6, 1, 1, 18, 1, 1, 3, 20, 20, 20, 20, 20] 96 rigid atoms, others: [2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 24, 25, 27, 28] set([0, 1, 34, 33, 32, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 26, 29, 30, 31]) total number of confs: 81 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042786 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042786 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042786/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042786 Building REAL250005042787 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042787' /scratch/stefan/7921153/working/building/REAL250005042787 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042787 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042787/0 /scratch/stefan/7921153/working/building/REAL250005042787 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 898) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/898 `/scratch/stefan/7921153/working/3D/898' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(O)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O) `REAL250005042787.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042787/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:2-3 Rotatable hydrogens reported. Reducing confs by a factor of 3 WARNING:root:Setting energy window to 12 and max confs to 66 ('energy: ', 12.0) ('conf: ', 66) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042787 none CC(C)(O)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 594 conformations in input total number of sets (complete confs): 594 using faster count positions algorithm for large data unique positions, atoms: [66, 45, 66, 66, 45, 45, 21, 21, 21, 21, 9, 1, 9, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 66, 66, 66, 66, 66, 66, 198, 45, 21, 21, 1, 21, 21, 63] 594 rigid atoms, others: [33, 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, 34, 35, 36]) total number of confs: 476 number of broken/clashed sets: 30 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042787 none CC(C)(O)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 594 conformations in input total number of sets (complete confs): 594 using faster count positions algorithm for large data unique positions, atoms: [27, 5, 27, 27, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 21, 21, 21, 21, 21, 1, 1, 1, 1, 27, 27, 27, 27, 27, 27, 81, 5, 1, 1, 21, 1, 1, 6] 594 rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 33, 36]) total number of confs: 208 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042787 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042787 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042787/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042787 Building REAL250005042788 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042788' /scratch/stefan/7921153/working/building/REAL250005042788 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042788 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042788/0 /scratch/stefan/7921153/working/building/REAL250005042788 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 899) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/899 `/scratch/stefan/7921153/working/3D/899' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O) `REAL250005042788.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042788/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042788 none CC1=CC1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 375 conformations in input total number of sets (complete confs): 375 using faster count positions algorithm for large data unique positions, atoms: [125, 125, 125, 60, 60, 60, 32, 31, 32, 31, 9, 1, 9, 1, 1, 1, 1, 1, 1, 31, 31, 32, 32, 125, 125, 125, 125, 125, 60, 31, 31, 1, 31, 31, 95] 375 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 31] 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, 32, 33, 34]) total number of confs: 429 number of broken/clashed sets: 63 ./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: REAL250005042788 none CC1=CC1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 375 conformations in input total number of sets (complete confs): 375 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 6, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 31, 31, 31, 31, 31, 1, 1, 1, 1, 50, 50, 50, 50, 50, 6, 1, 1, 31, 1, 1, 3] 375 rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 29, 30] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 34, 23, 24, 25, 26, 27, 28, 31]) total number of confs: 157 number of broken/clashed sets: 63 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042788 none CC1=CC1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 375 conformations in input total number of sets (complete confs): 375 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 13, 13, 13, 50, 50, 50, 50, 99, 99, 125, 125, 125, 125, 125, 50, 50, 50, 50, 2, 2, 2, 1, 1, 13, 50, 50, 125, 50, 50, 150] 375 rigid atoms, others: [0, 1, 2, 3, 4, 26, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 489 number of broken/clashed sets: 63 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042788 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042788 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042788/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042788 Building REAL250005042789 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042789' /scratch/stefan/7921153/working/building/REAL250005042789 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042789 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042789/0 /scratch/stefan/7921153/working/building/REAL250005042789 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 900) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/900 `/scratch/stefan/7921153/working/3D/900' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](O)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O) `REAL250005042789.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042789/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:2-3 Rotatable hydrogens reported. Reducing confs by a factor of 3 WARNING:root:Setting energy window to 12 and max confs to 66 ('energy: ', 12.0) ('conf: ', 66) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042789 none C[C@@H](O)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 423 conformations in input total number of sets (complete confs): 423 using faster count positions algorithm for large data unique positions, atoms: [47, 32, 47, 47, 32, 32, 21, 21, 21, 21, 8, 1, 8, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 47, 47, 47, 141, 32, 21, 21, 1, 21, 21, 63] 423 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33]) total number of confs: 359 number of broken/clashed sets: 27 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042789 none C[C@@H](O)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 423 conformations in input total number of sets (complete confs): 423 using faster count positions algorithm for large data unique positions, atoms: [23, 5, 23, 23, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 21, 21, 21, 21, 21, 1, 1, 1, 1, 23, 23, 23, 69, 5, 1, 1, 21, 1, 1, 6] 423 rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 28, 29, 31] set([0, 1, 2, 3, 4, 5, 33, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 30]) total number of confs: 186 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042789 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042789 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042789/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042789 Building REAL250005042790 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042790' /scratch/stefan/7921153/working/building/REAL250005042790 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042790 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042790/0 /scratch/stefan/7921153/working/building/REAL250005042790 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 901) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/901 `/scratch/stefan/7921153/working/3D/901' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(C=CCO)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O) `REAL250005042790.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042790/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:2-3 Rotatable hydrogens reported. Reducing confs by a factor of 3 WARNING:root:Setting energy window to 12 and max confs to 66 ('energy: ', 12.0) ('conf: ', 66) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042790 none O=C(C=CCO)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 1, 1, 5, 12, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 7, 7, 7, 4, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 35, 65, 65, 67, 14, 14, 14, 13, 5, 1, 5, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 65, 65, 67, 67, 201, 35, 13, 13, 1, 14, 14, 42] 603 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 31] 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, 32, 33, 34]) total number of confs: 436 number of broken/clashed sets: 99 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042790 none O=C(C=CCO)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 1, 1, 5, 12, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 7, 7, 7, 4, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 27, 27, 49, 1, 1, 1, 1, 1, 1, 5, 5, 13, 13, 13, 14, 14, 1, 1, 1, 1, 27, 27, 49, 49, 147, 6, 1, 1, 13, 1, 1, 6] 603 rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 29, 30] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 34, 23, 24, 25, 26, 27, 28, 31]) total number of confs: 346 number of broken/clashed sets: 99 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042790 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042790 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042790/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042790 Building REAL250005042791 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042791' /scratch/stefan/7921153/working/building/REAL250005042791 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042791 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042791/0 /scratch/stefan/7921153/working/building/REAL250005042791 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 902) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/902 `/scratch/stefan/7921153/working/3D/902' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O)C1=CCC1) `REAL250005042791.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042791.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042791/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042791 none O=C(N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O)C1=CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 1, 1, 5, 5, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 14, 14, 14, 14, 30, 30, 35, 35, 35, 35, 35, 14, 14, 14, 14, 1, 1, 1, 1, 7, 14, 14, 35, 14, 14, 42, 1, 1, 1, 1, 1] 105 rigid atoms, others: [32, 1, 34, 33, 19, 20, 21, 22, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 135 number of broken/clashed sets: 11 ./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: REAL250005042791 none O=C(N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O)C1=CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 1, 1, 5, 5, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 22, 22, 22, 21, 8, 1, 8, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 35, 35, 35, 35, 35, 21, 21, 1, 22, 22, 66, 35, 35, 35, 35, 35] 105 rigid atoms, others: [7, 9, 10, 11, 12, 13, 14, 26] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 151 number of broken/clashed sets: 11 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042791 none O=C(N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O)C1=CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 1, 1, 5, 5, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 1, 1, 1, 1, 1, 1, 6, 6, 21, 21, 21, 21, 21, 1, 1, 1, 1, 5, 14, 14, 14, 5, 1, 1, 21, 1, 1, 3, 14, 14, 14, 14, 14] 105 rigid atoms, others: [2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 24, 25, 27, 28] set([0, 1, 34, 33, 32, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 26, 29, 30, 31]) total number of confs: 60 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042791 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042791 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042791/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042791 Building REAL250005042792 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042792' /scratch/stefan/7921153/working/building/REAL250005042792 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042792 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042792/0 /scratch/stefan/7921153/working/building/REAL250005042792 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 903) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/903 `/scratch/stefan/7921153/working/3D/903' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CON=CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O) `REAL250005042792.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042792/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042792 none CON=CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 8, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [38, 38, 38, 28, 28, 28, 16, 16, 16, 16, 7, 1, 7, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 38, 38, 38, 38, 28, 16, 16, 1, 16, 16, 48] 114 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33]) total number of confs: 152 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042792 none CON=CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 8, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [24, 19, 19, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 16, 16, 16, 16, 16, 1, 1, 1, 1, 24, 24, 24, 19, 5, 1, 1, 16, 1, 1, 6] 114 rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 28, 29, 31] set([0, 1, 2, 3, 4, 5, 33, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 30]) total number of confs: 89 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042792 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042792 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042792/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042792 Building REAL250005042793 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042793' /scratch/stefan/7921153/working/building/REAL250005042793 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042793 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042793/0 /scratch/stefan/7921153/working/building/REAL250005042793 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 904) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/904 `/scratch/stefan/7921153/working/3D/904' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O)C1(F)CC1) `REAL250005042793.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042793.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042793/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042793 none O=C(N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O)C1(F)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 5, 15, 5, 5, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 219 conformations in input total number of sets (complete confs): 219 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 26, 26, 26, 26, 69, 69, 73, 73, 73, 73, 73, 26, 26, 26, 26, 1, 1, 1, 1, 12, 26, 26, 73, 26, 26, 78, 1, 1, 1, 1] 219 rigid atoms, others: [32, 1, 33, 19, 20, 21, 22, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 271 number of broken/clashed sets: 7 ./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: REAL250005042793 none O=C(N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O)C1(F)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 5, 15, 5, 5, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 219 conformations in input total number of sets (complete confs): 219 using faster count positions algorithm for large data unique positions, atoms: [43, 43, 22, 22, 22, 22, 8, 1, 8, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 43, 73, 73, 73, 43, 22, 22, 1, 22, 22, 66, 73, 73, 73, 73] 219 rigid atoms, others: [7, 9, 10, 11, 12, 13, 14, 26] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 266 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042793 none O=C(N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O)C1(F)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 5, 15, 5, 5, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 219 conformations in input total number of sets (complete confs): 219 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 22, 22, 22, 22, 22, 1, 1, 1, 1, 5, 26, 26, 26, 5, 1, 1, 22, 1, 1, 6, 26, 26, 26, 26] 219 rigid atoms, others: [2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 24, 25, 27, 28] set([0, 1, 33, 32, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 26, 29, 30, 31]) total number of confs: 102 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042793 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042793 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042793/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042793 Building REAL250005042794 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042794' /scratch/stefan/7921153/working/building/REAL250005042794 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042794 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042794/0 /scratch/stefan/7921153/working/building/REAL250005042794 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 905) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/905 `/scratch/stefan/7921153/working/3D/905' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=C(F)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O) `REAL250005042794.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042794.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042794/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042794 none CC=C(F)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 15, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [56, 56, 43, 56, 43, 43, 24, 24, 24, 23, 8, 1, 8, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 56, 56, 56, 56, 43, 23, 23, 1, 24, 24, 72] 168 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33]) total number of confs: 218 number of broken/clashed sets: 25 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042794 none CC=C(F)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 15, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [25, 25, 6, 25, 6, 6, 1, 1, 1, 1, 1, 1, 5, 5, 23, 23, 23, 23, 23, 1, 1, 1, 1, 25, 25, 25, 25, 6, 1, 1, 24, 1, 1, 3] 168 rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 28, 29, 31] set([0, 1, 2, 3, 4, 5, 33, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 30]) total number of confs: 99 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042794 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042794 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042794/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042794 Building REAL250005042795 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042795' /scratch/stefan/7921153/working/building/REAL250005042795 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042795 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042795/0 /scratch/stefan/7921153/working/building/REAL250005042795 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 906) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/906 `/scratch/stefan/7921153/working/3D/906' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CO)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O) `REAL250005042795.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042795/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:2-3 Rotatable hydrogens reported. Reducing confs by a factor of 3 WARNING:root:Setting energy window to 12 and max confs to 66 ('energy: ', 12.0) ('conf: ', 66) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042795 none CC(CO)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [65, 33, 65, 67, 33, 33, 14, 14, 14, 14, 6, 1, 6, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 65, 65, 65, 65, 67, 67, 201, 33, 14, 14, 1, 14, 14, 42] 603 rigid atoms, others: [33, 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, 34, 35, 36]) total number of confs: 481 number of broken/clashed sets: 100 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042795 none CC(CO)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [25, 5, 25, 43, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 14, 14, 14, 14, 14, 1, 1, 1, 1, 25, 25, 25, 25, 43, 43, 129, 5, 1, 1, 14, 1, 1, 6] 603 rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 33, 36]) total number of confs: 335 number of broken/clashed sets: 100 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042795 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042795 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042795/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042795 Building REAL250005042796 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042796' /scratch/stefan/7921153/working/building/REAL250005042796 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042796 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042796/0 /scratch/stefan/7921153/working/building/REAL250005042796 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 907) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/907 `/scratch/stefan/7921153/working/3D/907' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](O)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O) `REAL250005042796.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042796/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:2-3 Rotatable hydrogens reported. Reducing confs by a factor of 3 WARNING:root:Setting energy window to 12 and max confs to 66 ('energy: ', 12.0) ('conf: ', 66) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042796 none C[C@H](O)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 378 conformations in input total number of sets (complete confs): 378 using faster count positions algorithm for large data unique positions, atoms: [42, 30, 42, 42, 30, 30, 17, 17, 17, 16, 6, 1, 6, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 42, 42, 42, 126, 30, 16, 16, 1, 17, 17, 51] 378 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33]) total number of confs: 315 number of broken/clashed sets: 63 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042796 none C[C@H](O)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 378 conformations in input total number of sets (complete confs): 378 using faster count positions algorithm for large data unique positions, atoms: [29, 6, 29, 29, 6, 6, 1, 1, 1, 1, 1, 1, 5, 5, 16, 16, 16, 16, 16, 1, 1, 1, 1, 29, 29, 29, 87, 6, 1, 1, 16, 1, 1, 3] 378 rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 28, 29, 31] set([0, 1, 2, 3, 4, 5, 33, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 30]) total number of confs: 212 number of broken/clashed sets: 63 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042796 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042796 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042796/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042796 Building REAL250005042797 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042797' /scratch/stefan/7921153/working/building/REAL250005042797 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042797 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042797/0 /scratch/stefan/7921153/working/building/REAL250005042797 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 908) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/908 `/scratch/stefan/7921153/working/3D/908' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C1CC1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O) `REAL250005042797.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042797.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042797/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042797 none C=C1CC1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 336 conformations in input total number of sets (complete confs): 336 using faster count positions algorithm for large data unique positions, atoms: [112, 112, 112, 52, 52, 52, 29, 29, 29, 28, 9, 1, 9, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 112, 112, 112, 112, 112, 52, 28, 28, 1, 29, 29, 87] 336 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 31] 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, 32, 33, 34]) total number of confs: 384 number of broken/clashed sets: 17 ./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: REAL250005042797 none C=C1CC1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 336 conformations in input total number of sets (complete confs): 336 using faster count positions algorithm for large data unique positions, atoms: [41, 41, 41, 5, 5, 5, 1, 1, 1, 1, 1, 1, 6, 6, 28, 28, 28, 28, 28, 1, 1, 1, 1, 41, 41, 41, 41, 41, 5, 1, 1, 29, 1, 1, 3] 336 rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 29, 30] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 34, 23, 24, 25, 26, 27, 28, 31]) total number of confs: 136 number of broken/clashed sets: 17 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042797 none C=C1CC1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 336 conformations in input total number of sets (complete confs): 336 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 13, 13, 13, 41, 41, 41, 41, 94, 94, 112, 112, 112, 112, 112, 41, 41, 41, 41, 1, 1, 1, 1, 1, 13, 41, 41, 112, 41, 41, 123] 336 rigid atoms, others: [0, 1, 2, 3, 4, 23, 24, 25, 26, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 428 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042797 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042797 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042797/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042797 Building REAL250005042798 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042798' /scratch/stefan/7921153/working/building/REAL250005042798 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042798 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042798/0 /scratch/stefan/7921153/working/building/REAL250005042798 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 909) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/909 `/scratch/stefan/7921153/working/3D/909' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C(C)CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O) `REAL250005042798.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042798/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042798 none C=C(C)CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 315 conformations in input total number of sets (complete confs): 315 using faster count positions algorithm for large data unique positions, atoms: [105, 105, 105, 52, 52, 52, 27, 27, 27, 27, 9, 1, 9, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 105, 105, 105, 105, 105, 105, 105, 52, 27, 27, 1, 27, 27, 81] 315 rigid atoms, others: [33, 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, 34, 35, 36]) total number of confs: 463 number of broken/clashed sets: 30 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042798 none C=C(C)CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 315 conformations in input total number of sets (complete confs): 315 using faster count positions algorithm for large data unique positions, atoms: [56, 42, 56, 5, 5, 5, 1, 1, 1, 1, 1, 1, 6, 6, 27, 27, 27, 27, 27, 1, 1, 1, 1, 56, 56, 56, 56, 56, 42, 42, 5, 1, 1, 27, 1, 1, 3] 315 rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 33, 36]) total number of confs: 226 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042798 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042798 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042798/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042798 Building REAL250005042799 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042799' /scratch/stefan/7921153/working/building/REAL250005042799 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042799 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042799/0 /scratch/stefan/7921153/working/building/REAL250005042799 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 910) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/910 `/scratch/stefan/7921153/working/3D/910' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O) `REAL250005042799.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042799/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042799 none CC=CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 117 conformations in input total number of sets (complete confs): 117 using faster count positions algorithm for large data unique positions, atoms: [39, 39, 33, 33, 33, 18, 18, 18, 18, 6, 1, 6, 1, 1, 1, 1, 1, 1, 17, 17, 17, 18, 39, 39, 39, 39, 39, 33, 18, 18, 1, 17, 17, 54] 117 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33]) total number of confs: 160 number of broken/clashed sets: 18 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042799 none CC=CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 117 conformations in input total number of sets (complete confs): 117 using faster count positions algorithm for large data unique positions, atoms: [23, 23, 6, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 18, 18, 18, 18, 17, 1, 1, 1, 1, 23, 23, 23, 23, 23, 6, 1, 1, 18, 1, 1, 3] 117 rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 28, 29, 31] set([0, 1, 2, 3, 4, 33, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 30]) total number of confs: 89 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042799 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042799 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042799/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042799 Building REAL250005042800 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042800' /scratch/stefan/7921153/working/building/REAL250005042800 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042800 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042800/0 /scratch/stefan/7921153/working/building/REAL250005042800 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 911) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/911 `/scratch/stefan/7921153/working/3D/911' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H]1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O) `REAL250005042800.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042800.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042800/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042800 none C[C@@H]1C[C@H]1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 288 conformations in input total number of sets (complete confs): 288 using faster count positions algorithm for large data unique positions, atoms: [96, 96, 96, 96, 56, 96, 56, 56, 28, 28, 28, 28, 10, 1, 10, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 96, 96, 96, 96, 96, 56, 28, 28, 1, 28, 28, 84] 288 rigid atoms, others: [33, 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, 34, 35, 36]) total number of confs: 356 number of broken/clashed sets: 43 ./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: REAL250005042800 none C[C@@H]1C[C@H]1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 288 conformations in input total number of sets (complete confs): 288 using faster count positions algorithm for large data unique positions, atoms: [41, 41, 41, 41, 6, 41, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 28, 28, 28, 28, 28, 1, 1, 1, 1, 41, 41, 41, 41, 41, 6, 1, 1, 28, 1, 1, 3] 288 rigid atoms, others: [32, 34, 35, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 33, 36]) total number of confs: 136 number of broken/clashed sets: 43 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042800 none C[C@@H]1C[C@H]1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 288 conformations in input total number of sets (complete confs): 288 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 41, 41, 41, 41, 77, 77, 96, 96, 96, 96, 96, 41, 41, 41, 41, 2, 2, 2, 1, 1, 13, 41, 41, 96, 41, 41, 123] 288 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 389 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042800 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042800 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042800/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042800 Building REAL250005042801 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042801' /scratch/stefan/7921153/working/building/REAL250005042801 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042801 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042801/0 /scratch/stefan/7921153/working/building/REAL250005042801 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 912) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/912 `/scratch/stefan/7921153/working/3D/912' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O)C1(O)CC1) `REAL250005042801.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042801.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042801/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:2-3 Rotatable hydrogens reported. Reducing confs by a factor of 3 WARNING:root:Setting energy window to 12 and max confs to 66 ('energy: ', 12.0) ('conf: ', 66) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042801 none O=C(N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O)C1(O)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 5, 12, 5, 5, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 35, 35, 35, 35, 61, 61, 67, 67, 67, 67, 67, 35, 35, 35, 35, 1, 1, 1, 1, 12, 35, 35, 67, 35, 35, 105, 6, 1, 1, 1, 1] 603 rigid atoms, others: [32, 1, 34, 33, 19, 20, 21, 22, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 300 number of broken/clashed sets: 60 ./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: REAL250005042801 none O=C(N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O)C1(O)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 5, 12, 5, 5, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [52, 52, 21, 21, 21, 21, 7, 1, 7, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 52, 67, 67, 67, 52, 21, 21, 1, 21, 21, 63, 201, 67, 67, 67, 67] 603 rigid atoms, others: [7, 9, 10, 11, 12, 13, 14, 26] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 444 number of broken/clashed sets: 60 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042801 none O=C(N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1O)C1(O)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 12, 5, 12, 5, 5, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 1, 1, 1, 1, 1, 1, 6, 6, 21, 21, 21, 21, 21, 1, 1, 1, 1, 5, 35, 35, 35, 5, 1, 1, 21, 1, 1, 3, 105, 35, 35, 35, 35] 603 rigid atoms, others: [2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 24, 25, 27, 28] set([0, 1, 34, 33, 32, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 26, 29, 30, 31]) total number of confs: 220 number of broken/clashed sets: 60 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042801 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042801 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042801/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042801 Building REAL250005042802 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042802' /scratch/stefan/7921153/working/building/REAL250005042802 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042802 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042802/0 /scratch/stefan/7921153/working/building/REAL250005042802 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 913) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/913 `/scratch/stefan/7921153/working/3D/913' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1CC1)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1) `REAL250005042802.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042802.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042802/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042802 none O=C(CC1CC1)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [39, 18, 39, 62, 67, 67, 18, 18, 8, 18, 8, 1, 8, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 62, 62, 67, 67, 67, 67, 67, 18, 18, 8, 1, 54, 18, 18] 201 rigid atoms, others: [33, 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, 34, 35, 36]) total number of confs: 295 number of broken/clashed sets: 38 ./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: REAL250005042802 none O=C(CC1CC1)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 30, 38, 38, 1, 1, 1, 1, 1, 6, 6, 6, 18, 18, 18, 18, 18, 1, 1, 1, 1, 31, 31, 38, 38, 38, 38, 38, 1, 1, 6, 18, 3, 1, 1] 201 rigid atoms, others: [1, 35, 36, 6, 7, 8, 9, 10, 19, 20, 21, 22, 30, 31] set([0, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34]) total number of confs: 167 number of broken/clashed sets: 38 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042802 none O=C(CC1CC1)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 3, 1, 1, 1, 1, 15, 38, 38, 38, 38, 60, 60, 60, 67, 67, 67, 67, 67, 38, 38, 38, 38, 3, 3, 1, 1, 1, 1, 1, 38, 38, 60, 67, 114, 38, 38] 201 rigid atoms, others: [2, 3, 4, 5, 25, 26, 27, 28, 29] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 280 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042802 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042802 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042802/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042802 Building REAL250005042803 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042803' /scratch/stefan/7921153/working/building/REAL250005042803 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042803 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042803/0 /scratch/stefan/7921153/working/building/REAL250005042803 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 914) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/914 `/scratch/stefan/7921153/working/3D/914' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1) `REAL250005042803.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042803.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042803/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042803 none COCC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 165 conformations in input total number of sets (complete confs): 165 using faster count positions algorithm for large data unique positions, atoms: [55, 52, 29, 17, 29, 17, 17, 8, 17, 8, 1, 8, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 55, 55, 55, 52, 52, 17, 17, 9, 1, 51, 17, 17] 165 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33]) total number of confs: 256 number of broken/clashed sets: 30 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042803 none COCC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 165 conformations in input total number of sets (complete confs): 165 using faster count positions algorithm for large data unique positions, atoms: [33, 16, 4, 1, 3, 1, 1, 1, 1, 1, 6, 6, 6, 17, 17, 17, 17, 17, 1, 1, 1, 1, 33, 33, 33, 17, 17, 1, 1, 6, 17, 3, 1, 1] 165 rigid atoms, others: [32, 33, 3, 5, 6, 7, 8, 9, 18, 19, 20, 21, 27, 28] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 29, 30, 31]) total number of confs: 110 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042803 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042803 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042803/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042803 Building REAL250005042804 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042804' /scratch/stefan/7921153/working/building/REAL250005042804 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042804 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042804/0 /scratch/stefan/7921153/working/building/REAL250005042804 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 915) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/915 `/scratch/stefan/7921153/working/3D/915' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1) `REAL250005042804.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042804.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042804/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042804 none CCCC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [56, 54, 29, 17, 29, 17, 17, 9, 17, 9, 1, 9, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 56, 56, 56, 56, 56, 54, 54, 17, 17, 10, 1, 51, 17, 17] 168 rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35]) total number of confs: 257 number of broken/clashed sets: 37 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042804 none CCCC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [30, 21, 5, 1, 5, 1, 1, 1, 1, 1, 6, 6, 6, 17, 17, 17, 17, 17, 1, 1, 1, 1, 33, 33, 33, 32, 32, 22, 22, 1, 1, 6, 17, 3, 1, 1] 168 rigid atoms, others: [35, 34, 3, 5, 6, 7, 8, 9, 18, 19, 20, 21, 29, 30] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33]) total number of confs: 186 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042804 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042804 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042804/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042804 Building REAL250005042805 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042805' /scratch/stefan/7921153/working/building/REAL250005042805 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042805 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042805/0 /scratch/stefan/7921153/working/building/REAL250005042805 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 916) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/916 `/scratch/stefan/7921153/working/3D/916' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1) `REAL250005042805.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042805.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042805/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042805 none CC(C)CC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 35, 22, 15, 22, 15, 15, 9, 15, 9, 1, 9, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 35, 35, 35, 35, 35, 35, 35, 35, 35, 15, 15, 10, 1, 45, 15, 15] 105 rigid atoms, others: [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, 34, 36, 37, 38]) total number of confs: 171 number of broken/clashed sets: 25 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042805 none CC(C)CC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [20, 18, 21, 6, 1, 6, 1, 1, 1, 1, 1, 6, 6, 6, 15, 15, 15, 15, 14, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 21, 18, 18, 1, 1, 6, 15, 3, 1, 1] 105 rigid atoms, others: [32, 33, 4, 37, 6, 7, 8, 9, 10, 19, 20, 21, 22, 38] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36]) total number of confs: 116 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042805 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042805 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042805/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042805 Building REAL250005042806 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042806' /scratch/stefan/7921153/working/building/REAL250005042806 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042806 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042806/0 /scratch/stefan/7921153/working/building/REAL250005042806 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 917) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/917 `/scratch/stefan/7921153/working/3D/917' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC1C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1) `REAL250005042806.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042806.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042806/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042806 none CC1CC1C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [36, 36, 36, 28, 18, 28, 18, 18, 10, 18, 10, 1, 10, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 36, 36, 36, 36, 36, 36, 36, 18, 18, 10, 1, 54, 18, 18] 108 rigid atoms, others: [33, 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, 34, 35, 36]) total number of confs: 165 number of broken/clashed sets: 17 ./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: REAL250005042806 none CC1CC1C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [19, 19, 19, 7, 1, 7, 1, 1, 1, 1, 1, 5, 5, 5, 18, 18, 18, 18, 18, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19, 1, 1, 5, 18, 3, 1, 1] 108 rigid atoms, others: [35, 4, 6, 7, 8, 9, 10, 19, 20, 21, 22, 36, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34]) total number of confs: 79 number of broken/clashed sets: 17 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042806 none CC1CC1C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 108 conformations in input total number of sets (complete confs): 108 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 7, 7, 19, 19, 19, 19, 30, 30, 30, 36, 36, 36, 36, 36, 19, 19, 19, 19, 2, 2, 2, 1, 1, 1, 1, 19, 19, 30, 36, 57, 19, 19] 108 rigid atoms, others: [0, 1, 2, 3, 4, 26, 27, 28, 29] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 145 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042806 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042806 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042806/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042806 Building REAL250005042807 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042807' /scratch/stefan/7921153/working/building/REAL250005042807 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042807 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042807/0 /scratch/stefan/7921153/working/building/REAL250005042807 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 918) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/918 `/scratch/stefan/7921153/working/3D/918' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1) `REAL250005042807.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042807.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042807/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042807 none CCOCC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 366 conformations in input total number of sets (complete confs): 366 using faster count positions algorithm for large data unique positions, atoms: [122, 121, 96, 41, 23, 41, 23, 23, 9, 23, 9, 1, 9, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 122, 122, 122, 122, 122, 96, 96, 23, 23, 10, 1, 69, 23, 23] 366 rigid atoms, others: [33, 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, 34, 35, 36]) total number of confs: 484 number of broken/clashed sets: 79 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042807 none CCOCC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 366 conformations in input total number of sets (complete confs): 366 using faster count positions algorithm for large data unique positions, atoms: [70, 61, 25, 6, 1, 6, 1, 1, 1, 1, 1, 6, 6, 6, 23, 23, 23, 23, 23, 1, 1, 1, 1, 70, 70, 70, 70, 70, 26, 26, 1, 1, 6, 23, 3, 1, 1] 366 rigid atoms, others: [35, 4, 6, 7, 8, 9, 10, 19, 20, 21, 22, 36, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34]) total number of confs: 231 number of broken/clashed sets: 79 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042807 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042807 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042807/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042807 Building REAL250005042808 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042808' /scratch/stefan/7921153/working/building/REAL250005042808 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042808 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042808/0 /scratch/stefan/7921153/working/building/REAL250005042808 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 919) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/919 `/scratch/stefan/7921153/working/3D/919' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)=CC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1) `REAL250005042808.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042808.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042808/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042808 none CC(C)=CC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 5, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 33, 22, 12, 22, 12, 12, 8, 12, 8, 1, 8, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 33, 33, 33, 33, 33, 33, 33, 12, 12, 8, 1, 36, 12, 12] 99 rigid atoms, others: [33, 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, 34, 35, 36]) total number of confs: 137 number of broken/clashed sets: 22 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042808 none CC(C)=CC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 5, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 20, 6, 1, 6, 1, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 12, 12, 1, 1, 1, 1, 20, 20, 20, 20, 20, 20, 20, 1, 1, 6, 12, 6, 1, 1] 99 rigid atoms, others: [35, 4, 6, 7, 8, 9, 10, 19, 20, 21, 22, 36, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34]) total number of confs: 80 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042808 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042808 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042808/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042808 Building REAL250005042809 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042809' /scratch/stefan/7921153/working/building/REAL250005042809 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042809 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042809/0 /scratch/stefan/7921153/working/building/REAL250005042809 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 920) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/920 `/scratch/stefan/7921153/working/3D/920' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1) `REAL250005042809.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042809/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042809 none CCCCC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 315 conformations in input total number of sets (complete confs): 315 using faster count positions algorithm for large data unique positions, atoms: [105, 101, 93, 42, 20, 42, 20, 20, 8, 20, 8, 1, 8, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 105, 105, 105, 105, 105, 101, 101, 93, 93, 20, 20, 9, 1, 60, 20, 20] 315 rigid atoms, others: [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, 34, 36, 37, 38]) total number of confs: 466 number of broken/clashed sets: 65 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042809 none CCCCC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 315 conformations in input total number of sets (complete confs): 315 using faster count positions algorithm for large data unique positions, atoms: [62, 41, 31, 6, 1, 6, 1, 1, 1, 1, 1, 6, 6, 6, 20, 20, 20, 20, 20, 1, 1, 1, 1, 62, 63, 63, 61, 62, 44, 44, 32, 32, 1, 1, 6, 20, 3, 1, 1] 315 rigid atoms, others: [32, 33, 4, 37, 6, 7, 8, 9, 10, 19, 20, 21, 22, 38] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36]) total number of confs: 328 number of broken/clashed sets: 65 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042809 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042809 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042809/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042809 Building REAL250005042810 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042810' /scratch/stefan/7921153/working/building/REAL250005042810 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042810 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042810/0 /scratch/stefan/7921153/working/building/REAL250005042810 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 921) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/921 `/scratch/stefan/7921153/working/3D/921' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1) `REAL250005042810.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042810/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042810 none CC(C)C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 17, 11, 17, 11, 11, 8, 11, 8, 1, 8, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 17, 17, 17, 17, 17, 17, 17, 11, 11, 8, 1, 33, 11, 11] 51 rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35]) total number of confs: 82 number of broken/clashed sets: 11 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042810 none CC(C)C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [7, 4, 7, 1, 4, 1, 1, 1, 1, 1, 5, 5, 5, 11, 11, 11, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 1, 1, 5, 11, 3, 1, 1] 51 rigid atoms, others: [35, 34, 3, 5, 6, 7, 8, 9, 18, 19, 20, 21, 29, 30] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33]) total number of confs: 46 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042810 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042810 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042810/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042810 Building REAL250005042811 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042811' /scratch/stefan/7921153/working/building/REAL250005042811 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042811 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042811/0 /scratch/stefan/7921153/working/building/REAL250005042811 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 922) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/922 `/scratch/stefan/7921153/working/3D/922' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1) `REAL250005042811.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042811/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042811 none CCC(C)C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [36, 35, 29, 35, 16, 29, 16, 16, 9, 16, 9, 1, 9, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 36, 36, 36, 36, 36, 35, 35, 35, 35, 16, 16, 9, 1, 48, 16, 16] 108 rigid atoms, others: [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, 34, 36, 37, 38]) total number of confs: 169 number of broken/clashed sets: 24 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042811 none CCC(C)C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [20, 15, 7, 15, 1, 7, 1, 1, 1, 1, 1, 6, 6, 6, 16, 16, 16, 16, 16, 1, 1, 1, 1, 22, 22, 22, 22, 22, 15, 15, 15, 15, 1, 1, 6, 16, 3, 1, 1] 108 rigid atoms, others: [32, 33, 4, 37, 6, 7, 8, 9, 10, 19, 20, 21, 22, 38] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36]) total number of confs: 136 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042811 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042811 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042811/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042811 Building REAL250005042812 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042812' /scratch/stefan/7921153/working/building/REAL250005042812 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042812 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042812/0 /scratch/stefan/7921153/working/building/REAL250005042812 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 923) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/923 `/scratch/stefan/7921153/working/3D/923' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C)C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1) `REAL250005042812.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042812.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042812/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042812 none COC(C)C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 129 conformations in input total number of sets (complete confs): 129 using faster count positions algorithm for large data unique positions, atoms: [43, 42, 29, 42, 12, 29, 12, 12, 7, 12, 7, 1, 7, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 43, 43, 43, 42, 42, 42, 42, 12, 12, 7, 1, 36, 12, 12] 129 rigid atoms, others: [33, 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, 34, 35, 36]) total number of confs: 181 number of broken/clashed sets: 27 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042812 none COC(C)C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 129 conformations in input total number of sets (complete confs): 129 using faster count positions algorithm for large data unique positions, atoms: [27, 20, 7, 20, 1, 7, 1, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 12, 12, 1, 1, 1, 1, 27, 27, 27, 20, 20, 20, 20, 1, 1, 6, 12, 6, 1, 1] 129 rigid atoms, others: [35, 4, 6, 7, 8, 9, 10, 19, 20, 21, 22, 36, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34]) total number of confs: 108 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042812 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042812 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042812/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042812 Building REAL250005042813 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042813' /scratch/stefan/7921153/working/building/REAL250005042813 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042813 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042813/0 /scratch/stefan/7921153/working/building/REAL250005042813 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 924) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/924 `/scratch/stefan/7921153/working/3D/924' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCCC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1) `REAL250005042813.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042813/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042813 none C=CCCC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 318 conformations in input total number of sets (complete confs): 318 using faster count positions algorithm for large data unique positions, atoms: [106, 106, 94, 38, 19, 38, 19, 19, 8, 19, 8, 1, 8, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 106, 106, 106, 106, 106, 94, 94, 19, 19, 9, 1, 57, 19, 19] 318 rigid atoms, others: [33, 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, 34, 35, 36]) total number of confs: 460 number of broken/clashed sets: 67 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042813 none C=CCCC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 318 conformations in input total number of sets (complete confs): 318 using faster count positions algorithm for large data unique positions, atoms: [67, 45, 29, 6, 1, 6, 1, 1, 1, 1, 1, 6, 6, 6, 19, 19, 19, 19, 19, 1, 1, 1, 1, 67, 67, 67, 44, 44, 30, 30, 1, 1, 6, 19, 3, 1, 1] 318 rigid atoms, others: [35, 4, 6, 7, 8, 9, 10, 19, 20, 21, 22, 36, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34]) total number of confs: 297 number of broken/clashed sets: 67 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042813 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042813 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042813/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042813 Building REAL250005042814 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042814' /scratch/stefan/7921153/working/building/REAL250005042814 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042814 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042814/0 /scratch/stefan/7921153/working/building/REAL250005042814 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 925) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/925 `/scratch/stefan/7921153/working/3D/925' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C#N)C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1) `REAL250005042814.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042814.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042814/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042814 none CC(C#N)C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.1', 'N.1', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [24, 16, 24, 24, 14, 16, 14, 14, 8, 14, 9, 1, 9, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 24, 24, 24, 24, 14, 14, 9, 1, 42, 14, 14] 72 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33]) total number of confs: 134 number of broken/clashed sets: 17 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042814 none CC(C#N)C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.1', 'N.1', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [12, 5, 12, 12, 1, 5, 1, 1, 1, 1, 1, 6, 6, 6, 14, 14, 14, 14, 14, 1, 1, 1, 1, 12, 12, 12, 12, 1, 1, 6, 14, 3, 1, 1] 72 rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 19, 20, 21, 22, 27, 28] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 29, 30, 31]) total number of confs: 70 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042814 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042814 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042814/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042814 Building REAL250005042815 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042815' /scratch/stefan/7921153/working/building/REAL250005042815 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042815 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042815/0 /scratch/stefan/7921153/working/building/REAL250005042815 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 926) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/926 `/scratch/stefan/7921153/working/3D/926' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=C(C)C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1) `REAL250005042815.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042815/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042815 none CC=C(C)C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 129 conformations in input total number of sets (complete confs): 129 using faster count positions algorithm for large data unique positions, atoms: [43, 43, 33, 43, 17, 33, 17, 17, 11, 17, 11, 1, 11, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 43, 43, 43, 43, 43, 43, 43, 17, 17, 11, 1, 51, 17, 17] 129 rigid atoms, others: [33, 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, 34, 35, 36]) total number of confs: 180 number of broken/clashed sets: 20 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042815 none CC=C(C)C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 129 conformations in input total number of sets (complete confs): 129 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 7, 29, 1, 7, 1, 1, 1, 1, 1, 5, 5, 5, 17, 17, 17, 17, 17, 1, 1, 1, 1, 29, 29, 29, 29, 29, 29, 29, 1, 1, 5, 17, 3, 1, 1] 129 rigid atoms, others: [35, 4, 6, 7, 8, 9, 10, 19, 20, 21, 22, 36, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34]) total number of confs: 99 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042815 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042815 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042815/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042815 Building REAL250005042816 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042816' /scratch/stefan/7921153/working/building/REAL250005042816 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042816 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042816/0 /scratch/stefan/7921153/working/building/REAL250005042816 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 927) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/927 `/scratch/stefan/7921153/working/3D/927' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1) `REAL250005042816.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042816/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042816 none CCC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [25, 22, 18, 22, 18, 18, 9, 18, 10, 1, 10, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 25, 25, 25, 25, 25, 18, 18, 10, 1, 54, 18, 18] 75 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32]) total number of confs: 136 number of broken/clashed sets: 15 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042816 none CCC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [7, 3, 1, 3, 1, 1, 1, 1, 1, 6, 6, 6, 18, 18, 18, 18, 18, 1, 1, 1, 1, 8, 7, 7, 8, 8, 1, 1, 6, 18, 3, 1, 1] 75 rigid atoms, others: [32, 2, 4, 5, 6, 7, 8, 17, 18, 19, 20, 26, 27, 31] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 28, 29, 30]) total number of confs: 60 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042816 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042816 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042816/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042816 Building REAL250005042817 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042817' /scratch/stefan/7921153/working/building/REAL250005042817 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042817 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042817/0 /scratch/stefan/7921153/working/building/REAL250005042817 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 928) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/928 `/scratch/stefan/7921153/working/3D/928' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1) `REAL250005042817.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042817/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042817 none COCCC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 270 conformations in input total number of sets (complete confs): 270 using faster count positions algorithm for large data unique positions, atoms: [90, 90, 75, 34, 19, 34, 19, 19, 9, 19, 9, 1, 9, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 90, 90, 90, 90, 90, 75, 75, 19, 19, 10, 1, 57, 19, 19] 270 rigid atoms, others: [33, 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, 34, 35, 36]) total number of confs: 422 number of broken/clashed sets: 59 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042817 none COCCC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 270 conformations in input total number of sets (complete confs): 270 using faster count positions algorithm for large data unique positions, atoms: [61, 37, 21, 6, 1, 6, 1, 1, 1, 1, 1, 6, 6, 6, 19, 19, 19, 19, 19, 1, 1, 1, 1, 61, 61, 61, 36, 36, 22, 22, 1, 1, 6, 19, 3, 1, 1] 270 rigid atoms, others: [35, 4, 6, 7, 8, 9, 10, 19, 20, 21, 22, 36, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34]) total number of confs: 228 number of broken/clashed sets: 59 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042817 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042817 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042817/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042817 Building REAL250005042818 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042818' /scratch/stefan/7921153/working/building/REAL250005042818 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042818 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042818/0 /scratch/stefan/7921153/working/building/REAL250005042818 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 929) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/929 `/scratch/stefan/7921153/working/3D/929' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1) `REAL250005042818.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042818.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042818/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042818 none CC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [8, 6, 8, 6, 6, 5, 6, 5, 1, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 8, 8, 8, 6, 6, 5, 1, 18, 6, 6] 24 rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29]) total number of confs: 41 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042818 none CC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 4, 4, 4, 6, 6, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 1, 1, 4, 6, 6, 1, 1] 24 rigid atoms, others: [1, 3, 4, 5, 6, 7, 16, 17, 18, 19, 23, 24, 28, 29] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 25, 26, 27]) total number of confs: 28 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042818 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042818 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042818/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042818 Building REAL250005042819 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042819' /scratch/stefan/7921153/working/building/REAL250005042819 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042819 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042819/0 /scratch/stefan/7921153/working/building/REAL250005042819 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 930) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/930 `/scratch/stefan/7921153/working/3D/930' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CN(C(=O)C2CC2)C[C@@H]1O)C1=CC(=O)[N-]O1) `REAL250005042819.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042819/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042819 none O=C(N[C@@H]1CN(C(=O)C2CC2)C[C@@H]1O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 12, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [9, 1, 9, 9, 13, 13, 13, 13, 16, 16, 24, 24, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 9, 13, 13, 24, 24, 24, 24, 24, 13, 13, 39, 1] 72 rigid atoms, others: [1, 33, 16, 17, 18, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 112 number of broken/clashed sets: 15 ./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: REAL250005042819 none O=C(N[C@@H]1CN(C(=O)C2CC2)C[C@@H]1O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 12, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [21, 21, 15, 15, 15, 15, 8, 1, 8, 1, 1, 1, 15, 15, 15, 15, 21, 24, 24, 24, 24, 24, 21, 15, 15, 1, 1, 1, 1, 1, 15, 15, 45, 24] 72 rigid atoms, others: [7, 9, 10, 11, 25, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 30, 31, 32, 33]) total number of confs: 101 number of broken/clashed sets: 15 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042819 none O=C(N[C@@H]1CN(C(=O)C2CC2)C[C@@H]1O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 12, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [6, 6, 1, 1, 1, 1, 1, 1, 4, 4, 15, 15, 1, 1, 1, 1, 6, 13, 13, 13, 13, 13, 6, 1, 1, 15, 15, 15, 15, 15, 1, 1, 3, 13] 72 rigid atoms, others: [2, 3, 4, 5, 6, 7, 12, 13, 14, 15, 23, 24, 30, 31] set([0, 1, 33, 32, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29]) total number of confs: 61 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042819 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042819 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042819/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042819 Building REAL250005042820 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042820' /scratch/stefan/7921153/working/building/REAL250005042820 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042820 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042820/0 /scratch/stefan/7921153/working/building/REAL250005042820 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 931) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/931 `/scratch/stefan/7921153/working/3D/931' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CN(C(=O)C2CCC2)C[C@@H]1O)C1=CC(=O)[N-]O1) `REAL250005042820.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042820/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042820 none O=C(N[C@@H]1CN(C(=O)C2CCC2)C[C@@H]1O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 12, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 17, 17, 17, 17, 25, 25, 33, 33, 33, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1, 8, 17, 17, 33, 33, 33, 33, 33, 33, 33, 17, 17, 51, 1] 99 rigid atoms, others: [1, 36, 17, 18, 19, 20, 21, 22] set([0, 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]) total number of confs: 154 number of broken/clashed sets: 14 ./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: REAL250005042820 none O=C(N[C@@H]1CN(C(=O)C2CCC2)C[C@@H]1O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 12, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 15, 15, 15, 15, 8, 1, 8, 1, 1, 1, 1, 15, 15, 15, 15, 28, 33, 33, 33, 33, 33, 28, 15, 15, 1, 1, 1, 1, 1, 1, 1, 15, 15, 45, 33] 99 rigid atoms, others: [32, 7, 9, 10, 11, 12, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 33, 34, 35, 36]) total number of confs: 128 number of broken/clashed sets: 14 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042820 none O=C(N[C@@H]1CN(C(=O)C2CCC2)C[C@@H]1O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 12, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 15, 15, 15, 1, 1, 1, 1, 5, 17, 17, 17, 17, 17, 5, 1, 1, 15, 15, 15, 15, 15, 15, 15, 1, 1, 6, 17] 99 rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 13, 14, 15, 34, 24, 25, 16] set([0, 1, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 35, 36]) total number of confs: 73 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042820 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042820 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042820/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042820 Building REAL250005042821 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042821' /scratch/stefan/7921153/working/building/REAL250005042821 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042821 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042821/0 /scratch/stefan/7921153/working/building/REAL250005042821 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 932) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/932 `/scratch/stefan/7921153/working/3D/932' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1) `REAL250005042821.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042821/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042821 none NC(=O)C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 6, 6, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [4, 7, 6, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [20, 19, 20, 11, 19, 11, 11, 6, 11, 6, 1, 6, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 20, 20, 11, 11, 6, 1, 33, 11, 11] 60 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30]) total number of confs: 94 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042821 none NC(=O)C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 6, 6, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [4, 7, 6, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [12, 4, 12, 1, 4, 1, 1, 1, 1, 1, 5, 5, 5, 11, 11, 11, 11, 11, 1, 1, 1, 1, 12, 12, 1, 1, 5, 11, 6, 1, 1] 60 rigid atoms, others: [3, 5, 6, 7, 8, 9, 18, 19, 20, 21, 24, 25, 29, 30] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 26, 27, 28]) total number of confs: 56 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042821 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042821 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042821/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042821 Building REAL250005042822 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042822' /scratch/stefan/7921153/working/building/REAL250005042822 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042822 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042822/0 /scratch/stefan/7921153/working/building/REAL250005042822 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 933) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/933 `/scratch/stefan/7921153/working/3D/933' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1) `REAL250005042822.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042822/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042822 none CC(C)(C)C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 6, 10, 6, 6, 4, 6, 4, 1, 4, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 6, 4, 1, 18, 6, 6] 30 rigid atoms, others: [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, 34, 36, 37, 38]) total number of confs: 49 number of broken/clashed sets: 30 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042822 none CC(C)(C)C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 4, 4, 4, 6, 6, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 4, 6, 3, 1, 1] 30 rigid atoms, others: [32, 33, 4, 37, 6, 7, 8, 9, 10, 19, 20, 21, 22, 38] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36]) total number of confs: 21 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042822 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042822 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042822/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042822 Building REAL250005042823 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042823' /scratch/stefan/7921153/working/building/REAL250005042823 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042823 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042823/0 /scratch/stefan/7921153/working/building/REAL250005042823 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 934) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/934 `/scratch/stefan/7921153/working/3D/934' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C(=O)N2C[C@@H](NC(=O)C3=CC(=O)[N-]O3)[C@@H](O)C2)CC1) `REAL250005042823.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042823/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042823 none CC1(C(=O)N2C[C@@H](NC(=O)C3=CC(=O)[N-]O3)[C@@H](O)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 8, 19, 8, 8, 6, 8, 6, 1, 6, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 19, 19, 19, 19, 19, 8, 8, 6, 1, 24, 8, 8, 19, 19, 19, 19] 57 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 73 number of broken/clashed sets: 15 ./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: REAL250005042823 none CC1(C(=O)N2C[C@@H](NC(=O)C3=CC(=O)[N-]O3)[C@@H](O)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [10, 7, 1, 7, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 8, 8, 8, 1, 1, 1, 1, 10, 10, 10, 10, 10, 1, 1, 5, 8, 6, 1, 1, 10, 10, 10, 10] 57 rigid atoms, others: [32, 2, 4, 5, 6, 7, 8, 17, 18, 19, 20, 26, 27, 31] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 28, 29, 30, 33, 34, 35, 36]) total number of confs: 48 number of broken/clashed sets: 15 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042823 none CC1(C(=O)N2C[C@@H](NC(=O)C3=CC(=O)[N-]O3)[C@@H](O)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 3, 3, 10, 10, 10, 10, 17, 17, 17, 19, 19, 19, 19, 19, 10, 10, 10, 10, 1, 1, 2, 2, 2, 10, 10, 17, 19, 30, 10, 10, 1, 1, 1, 1] 57 rigid atoms, others: [0, 1, 2, 35, 36, 33, 34, 21, 22] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 80 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042823 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042823 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042823/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042823 Building REAL250005042824 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042824' /scratch/stefan/7921153/working/building/REAL250005042824 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042824 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042824/0 /scratch/stefan/7921153/working/building/REAL250005042824 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 935) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/935 `/scratch/stefan/7921153/working/3D/935' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H]1C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1) `REAL250005042824.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042824.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042824/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042824 none C[C@@H]1C[C@H]1C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [37, 37, 37, 37, 31, 37, 18, 31, 18, 18, 8, 18, 8, 1, 8, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 37, 37, 37, 37, 37, 18, 18, 8, 1, 54, 18, 18] 111 rigid atoms, others: [33, 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, 34, 35, 36]) total number of confs: 165 number of broken/clashed sets: 17 ./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: REAL250005042824 none C[C@@H]1C[C@H]1C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 21, 21, 7, 21, 1, 7, 1, 1, 1, 1, 1, 5, 5, 5, 18, 18, 18, 18, 18, 1, 1, 1, 1, 21, 21, 21, 21, 21, 1, 1, 5, 18, 3, 1, 1] 111 rigid atoms, others: [35, 36, 6, 8, 9, 10, 11, 12, 21, 22, 23, 24, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 32, 33, 34]) total number of confs: 83 number of broken/clashed sets: 17 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042824 none C[C@@H]1C[C@H]1C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 8, 8, 21, 21, 21, 21, 32, 32, 32, 37, 37, 37, 37, 37, 21, 21, 21, 21, 2, 2, 2, 1, 1, 21, 21, 32, 37, 63, 21, 21] 111 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 156 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042824 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042824 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042824/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042824 Building REAL250005042825 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042825' /scratch/stefan/7921153/working/building/REAL250005042825 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042825 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042825/0 /scratch/stefan/7921153/working/building/REAL250005042825 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 936) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/936 `/scratch/stefan/7921153/working/3D/936' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@@H]1C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1) `REAL250005042825.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042825/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042825 none C[C@H]1C[C@@H]1C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [45, 45, 45, 45, 36, 45, 18, 36, 18, 18, 11, 18, 11, 1, 11, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 45, 45, 45, 45, 45, 18, 18, 11, 1, 54, 18, 18] 135 rigid atoms, others: [33, 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, 34, 35, 36]) total number of confs: 187 number of broken/clashed sets: 18 ./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: REAL250005042825 none C[C@H]1C[C@@H]1C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [21, 21, 21, 21, 6, 21, 1, 6, 1, 1, 1, 1, 1, 5, 5, 5, 18, 18, 18, 18, 18, 1, 1, 1, 1, 21, 21, 21, 21, 21, 1, 1, 5, 18, 6, 1, 1] 135 rigid atoms, others: [35, 36, 6, 8, 9, 10, 11, 12, 21, 22, 23, 24, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 32, 33, 34]) total number of confs: 88 number of broken/clashed sets: 18 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042825 none C[C@H]1C[C@@H]1C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 135 conformations in input total number of sets (complete confs): 135 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 8, 8, 21, 21, 21, 21, 37, 37, 37, 45, 45, 45, 45, 45, 21, 21, 21, 21, 2, 2, 2, 1, 1, 21, 21, 37, 45, 63, 21, 21] 135 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 171 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042825 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042825 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042825/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042825 Building REAL250005042826 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042826' /scratch/stefan/7921153/working/building/REAL250005042826 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042826 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042826/0 /scratch/stefan/7921153/working/building/REAL250005042826 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 937) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/937 `/scratch/stefan/7921153/working/3D/937' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CO)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1) `REAL250005042826.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042826/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:2-3 Rotatable hydrogens reported. Reducing confs by a factor of 3 WARNING:root:Setting energy window to 12 and max confs to 66 ('energy: ', 12.0) ('conf: ', 66) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042826 none O=C(CO)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 7, 7, 6, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [6, 7, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 207 conformations in input total number of sets (complete confs): 207 using faster count positions algorithm for large data unique positions, atoms: [17, 14, 17, 23, 14, 14, 8, 14, 8, 1, 8, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 23, 23, 69, 14, 14, 9, 1, 42, 14, 14] 207 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30]) total number of confs: 196 number of broken/clashed sets: 66 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042826 none O=C(CO)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 7, 7, 6, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [6, 7, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 207 conformations in input total number of sets (complete confs): 207 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 12, 1, 1, 1, 1, 1, 6, 6, 6, 14, 14, 14, 14, 14, 1, 1, 1, 1, 12, 12, 36, 1, 1, 6, 14, 3, 1, 1] 207 rigid atoms, others: [1, 4, 5, 6, 7, 8, 17, 18, 19, 20, 24, 25, 29, 30] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 26, 27, 28]) total number of confs: 103 number of broken/clashed sets: 66 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042826 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042826 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042826/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042826 Building REAL250005042827 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042827' /scratch/stefan/7921153/working/building/REAL250005042827 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042827 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042827/0 /scratch/stefan/7921153/working/building/REAL250005042827 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 938) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/938 `/scratch/stefan/7921153/working/3D/938' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CN(C(=O)C2CCO2)C[C@@H]1O)C1=CC(=O)[N-]O1) `REAL250005042827.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042827.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042827/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042827 none O=C(N[C@@H]1CN(C(=O)C2CCO2)C[C@@H]1O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 7, 12, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 17, 17, 17, 17, 28, 28, 40, 40, 40, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1, 9, 17, 17, 40, 40, 40, 40, 40, 17, 17, 51, 1] 120 rigid atoms, others: [1, 34, 17, 18, 19, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 176 number of broken/clashed sets: 16 ./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: REAL250005042827 none O=C(N[C@@H]1CN(C(=O)C2CCO2)C[C@@H]1O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 7, 12, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [36, 36, 22, 22, 22, 22, 9, 1, 9, 1, 1, 1, 1, 22, 22, 22, 22, 36, 40, 40, 40, 40, 40, 36, 22, 22, 1, 1, 1, 1, 1, 22, 22, 66, 40] 120 rigid atoms, others: [7, 9, 10, 11, 12, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 31, 32, 33, 34]) total number of confs: 160 number of broken/clashed sets: 16 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042827 none O=C(N[C@@H]1CN(C(=O)C2CCO2)C[C@@H]1O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 7, 12, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 22, 22, 22, 1, 1, 1, 1, 5, 17, 17, 17, 17, 17, 5, 1, 1, 22, 22, 22, 22, 22, 1, 1, 6, 17] 120 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 24, 25, 31] set([0, 1, 34, 33, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30]) total number of confs: 89 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042827 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042827 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042827/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042827 Building REAL250005042828 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042828' /scratch/stefan/7921153/working/building/REAL250005042828 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042828 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042828/0 /scratch/stefan/7921153/working/building/REAL250005042828 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 939) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/939 `/scratch/stefan/7921153/working/3D/939' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CN(C(=O)C2COC2)C[C@@H]1O)C1=CC(=O)[N-]O1) `REAL250005042828.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042828.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042828/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042828 none O=C(N[C@@H]1CN(C(=O)C2COC2)C[C@@H]1O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 7, 12, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 84 conformations in input total number of sets (complete confs): 84 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 13, 13, 13, 13, 20, 20, 28, 28, 28, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 8, 13, 13, 28, 28, 28, 28, 28, 13, 13, 39, 1] 84 rigid atoms, others: [1, 34, 17, 18, 19, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 130 number of broken/clashed sets: 12 ./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: REAL250005042828 none O=C(N[C@@H]1CN(C(=O)C2COC2)C[C@@H]1O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 7, 12, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 84 conformations in input total number of sets (complete confs): 84 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 17, 17, 17, 17, 7, 1, 7, 1, 1, 1, 1, 17, 17, 17, 17, 24, 28, 28, 28, 28, 28, 24, 17, 17, 1, 1, 1, 1, 1, 17, 17, 51, 28] 84 rigid atoms, others: [7, 9, 10, 11, 12, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 31, 32, 33, 34]) total number of confs: 114 number of broken/clashed sets: 12 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042828 none O=C(N[C@@H]1CN(C(=O)C2COC2)C[C@@H]1O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 7, 12, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 84 conformations in input total number of sets (complete confs): 84 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 1, 1, 1, 1, 1, 1, 6, 6, 17, 17, 17, 1, 1, 1, 1, 5, 13, 13, 13, 13, 13, 5, 1, 1, 17, 17, 17, 17, 17, 1, 1, 3, 13] 84 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 24, 25, 31] set([0, 1, 34, 33, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30]) total number of confs: 69 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042828 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042828 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042828/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042828 Building REAL250005042829 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042829' /scratch/stefan/7921153/working/building/REAL250005042829 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042829 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042829/0 /scratch/stefan/7921153/working/building/REAL250005042829 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 940) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/940 `/scratch/stefan/7921153/working/3D/940' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(C=CCO)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1) `REAL250005042829.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042829.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042829/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:2-3 Rotatable hydrogens reported. Reducing confs by a factor of 3 WARNING:root:Setting energy window to 12 and max confs to 66 ('energy: ', 12.0) ('conf: ', 66) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042829 none O=C(C=CCO)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 1, 1, 5, 12, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 7, 7, 7, 7, 6, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [35, 18, 35, 66, 66, 67, 18, 18, 10, 18, 10, 1, 10, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 66, 66, 67, 67, 201, 18, 18, 10, 1, 54, 18, 18] 603 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 31] 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, 32, 33, 34]) total number of confs: 454 number of broken/clashed sets: 75 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042829 none O=C(C=CCO)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 1, 1, 5, 12, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 7, 7, 7, 7, 6, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 27, 27, 55, 1, 1, 1, 1, 1, 5, 5, 5, 18, 18, 18, 18, 18, 1, 1, 1, 1, 27, 27, 55, 55, 165, 1, 1, 5, 18, 6, 1, 1] 603 rigid atoms, others: [1, 34, 33, 6, 7, 8, 9, 10, 19, 20, 21, 22, 28, 29] set([0, 32, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 30, 31]) total number of confs: 391 number of broken/clashed sets: 75 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042829 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042829 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042829/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042829 Building REAL250005042830 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042830' /scratch/stefan/7921153/working/building/REAL250005042830 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042830 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042830/0 /scratch/stefan/7921153/working/building/REAL250005042830 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 941) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/941 `/scratch/stefan/7921153/working/3D/941' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC=CC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1) `REAL250005042830.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042830.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042830/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042830 none CCC=CC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [66, 57, 57, 35, 18, 35, 18, 18, 10, 18, 10, 1, 10, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 66, 66, 66, 66, 66, 57, 57, 18, 18, 10, 1, 54, 18, 18] 198 rigid atoms, others: [33, 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, 34, 35, 36]) total number of confs: 275 number of broken/clashed sets: 41 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042830 none CCC=CC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [41, 26, 25, 6, 1, 6, 1, 1, 1, 1, 1, 6, 6, 6, 18, 18, 18, 18, 18, 1, 1, 1, 1, 41, 41, 41, 41, 41, 25, 25, 1, 1, 6, 18, 3, 1, 1] 198 rigid atoms, others: [35, 4, 6, 7, 8, 9, 10, 19, 20, 21, 22, 36, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34]) total number of confs: 174 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042830 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042830 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042830/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042830 Building REAL250005042831 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042831' /scratch/stefan/7921153/working/building/REAL250005042831 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042831 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042831/0 /scratch/stefan/7921153/working/building/REAL250005042831 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 942) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/942 `/scratch/stefan/7921153/working/3D/942' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1) `REAL250005042831.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042831.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042831/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042831 none C#CCCC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 195 conformations in input total number of sets (complete confs): 195 using faster count positions algorithm for large data unique positions, atoms: [65, 65, 60, 29, 15, 29, 15, 15, 8, 15, 8, 1, 8, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 65, 65, 65, 60, 60, 15, 15, 9, 1, 45, 15, 15] 195 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 31] 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, 32, 33, 34]) total number of confs: 291 number of broken/clashed sets: 39 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042831 none C#CCCC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 195 conformations in input total number of sets (complete confs): 195 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 25, 6, 1, 6, 1, 1, 1, 1, 1, 6, 6, 6, 15, 15, 15, 15, 15, 1, 1, 1, 1, 35, 34, 34, 26, 26, 1, 1, 6, 15, 3, 1, 1] 195 rigid atoms, others: [33, 34, 4, 6, 7, 8, 9, 10, 19, 20, 21, 22, 28, 29] set([0, 1, 2, 3, 5, 32, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 30, 31]) total number of confs: 165 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042831 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042831 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042831/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042831 Building REAL250005042832 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042832' /scratch/stefan/7921153/working/building/REAL250005042832 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042832 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042832/0 /scratch/stefan/7921153/working/building/REAL250005042832 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 943) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/943 `/scratch/stefan/7921153/working/3D/943' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(O)C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1) `REAL250005042832.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042832.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042832/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:2-3 Rotatable hydrogens reported. Reducing confs by a factor of 3 WARNING:root:Setting energy window to 12 and max confs to 66 ('energy: ', 12.0) ('conf: ', 66) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042832 none C=CC(O)C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 7, 7, 7, 7, 6, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 396 conformations in input total number of sets (complete confs): 396 using faster count positions algorithm for large data unique positions, atoms: [44, 44, 25, 44, 12, 25, 12, 12, 7, 12, 7, 1, 7, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 44, 44, 44, 44, 132, 12, 12, 7, 1, 36, 12, 12] 396 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 31] 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, 32, 33, 34]) total number of confs: 331 number of broken/clashed sets: 89 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042832 none C=CC(O)C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 7, 7, 7, 7, 6, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 396 conformations in input total number of sets (complete confs): 396 using faster count positions algorithm for large data unique positions, atoms: [34, 21, 7, 21, 1, 7, 1, 1, 1, 1, 1, 5, 5, 5, 12, 12, 12, 12, 12, 1, 1, 1, 1, 34, 34, 34, 21, 63, 1, 1, 5, 12, 3, 1, 1] 396 rigid atoms, others: [33, 34, 4, 6, 7, 8, 9, 10, 19, 20, 21, 22, 28, 29] set([0, 1, 2, 3, 5, 32, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 30, 31]) total number of confs: 200 number of broken/clashed sets: 89 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042832 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042832 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042832/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042832 Building REAL250005042833 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042833' /scratch/stefan/7921153/working/building/REAL250005042833 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042833 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042833/0 /scratch/stefan/7921153/working/building/REAL250005042833 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 944) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/944 `/scratch/stefan/7921153/working/3D/944' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1) `REAL250005042833.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042833.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042833/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:2-3 Rotatable hydrogens reported. Reducing confs by a factor of 3 WARNING:root:Setting energy window to 12 and max confs to 66 ('energy: ', 12.0) ('conf: ', 66) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042833 none CC(O)C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 7, 7, 7, 7, 6, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 216 conformations in input total number of sets (complete confs): 216 using faster count positions algorithm for large data unique positions, atoms: [24, 16, 24, 10, 16, 10, 10, 5, 10, 6, 1, 6, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 24, 24, 24, 24, 72, 10, 10, 6, 1, 30, 10, 10] 216 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33]) total number of confs: 194 number of broken/clashed sets: 71 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042833 none CC(O)C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 7, 7, 7, 7, 6, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 216 conformations in input total number of sets (complete confs): 216 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 13, 1, 5, 1, 1, 1, 1, 1, 6, 6, 6, 10, 10, 10, 10, 10, 1, 1, 1, 1, 13, 13, 13, 13, 39, 1, 1, 6, 10, 3, 1, 1] 216 rigid atoms, others: [32, 33, 3, 5, 6, 7, 8, 9, 18, 19, 20, 21, 27, 28] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 29, 30, 31]) total number of confs: 102 number of broken/clashed sets: 71 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042833 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042833 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042833/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042833 Building REAL250005042834 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042834' /scratch/stefan/7921153/working/building/REAL250005042834 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042834 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042834/0 /scratch/stefan/7921153/working/building/REAL250005042834 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 945) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/945 `/scratch/stefan/7921153/working/3D/945' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1) `REAL250005042834.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042834.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042834/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042834 none CC(=O)C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [34, 22, 34, 14, 22, 14, 14, 9, 14, 9, 1, 9, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 34, 34, 34, 14, 14, 9, 1, 42, 14, 14] 102 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31]) total number of confs: 149 number of broken/clashed sets: 21 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042834 none CC(=O)C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [16, 5, 17, 1, 5, 1, 1, 1, 1, 1, 6, 6, 6, 14, 14, 14, 14, 14, 1, 1, 1, 1, 17, 17, 17, 1, 1, 6, 14, 6, 1, 1] 102 rigid atoms, others: [3, 5, 6, 7, 8, 9, 18, 19, 20, 21, 25, 26, 30, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 27, 28, 29]) total number of confs: 76 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042834 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042834 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042834/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042834 Building REAL250005042835 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042835' /scratch/stefan/7921153/working/building/REAL250005042835 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042835 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042835/0 /scratch/stefan/7921153/working/building/REAL250005042835 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 946) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/946 `/scratch/stefan/7921153/working/3D/946' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CN(C(=O)C2(F)CC2)C[C@@H]1O)C1=CC(=O)[N-]O1) `REAL250005042835.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042835/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042835 none O=C(N[C@@H]1CN(C(=O)C2(F)CC2)C[C@@H]1O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 5, 15, 5, 5, 5, 5, 7, 12, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [9, 1, 9, 9, 13, 13, 13, 13, 24, 24, 36, 36, 36, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 9, 13, 13, 36, 36, 36, 36, 13, 13, 39, 1] 108 rigid atoms, others: [1, 33, 17, 18, 19, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 152 number of broken/clashed sets: 24 ./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: REAL250005042835 none O=C(N[C@@H]1CN(C(=O)C2(F)CC2)C[C@@H]1O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 5, 15, 5, 5, 5, 5, 7, 12, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [29, 29, 19, 19, 19, 19, 8, 1, 8, 1, 1, 1, 1, 19, 19, 19, 19, 29, 36, 36, 36, 36, 36, 29, 19, 19, 1, 1, 1, 1, 19, 19, 57, 36] 108 rigid atoms, others: [7, 9, 10, 11, 12, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33]) total number of confs: 141 number of broken/clashed sets: 24 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042835 none O=C(N[C@@H]1CN(C(=O)C2(F)CC2)C[C@@H]1O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 5, 15, 5, 5, 5, 5, 7, 12, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [6, 6, 1, 1, 1, 1, 1, 1, 4, 4, 19, 19, 19, 1, 1, 1, 1, 6, 13, 13, 13, 13, 13, 6, 1, 1, 19, 19, 19, 19, 1, 1, 3, 13] 108 rigid atoms, others: [2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 24, 25, 30, 31] set([0, 1, 33, 32, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29]) total number of confs: 72 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042835 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042835 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042835/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042835 Building REAL250005042836 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042836' /scratch/stefan/7921153/working/building/REAL250005042836 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042836 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042836/0 /scratch/stefan/7921153/working/building/REAL250005042836 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 947) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/947 `/scratch/stefan/7921153/working/3D/947' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=C(F)C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1) `REAL250005042836.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042836.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042836/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042836 none CC=C(F)C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 15, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 96 conformations in input total number of sets (complete confs): 96 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 25, 32, 15, 25, 15, 15, 7, 15, 7, 1, 7, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 32, 32, 32, 32, 15, 15, 7, 1, 45, 15, 15] 96 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33]) total number of confs: 142 number of broken/clashed sets: 18 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042836 none CC=C(F)C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 15, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 96 conformations in input total number of sets (complete confs): 96 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 6, 22, 1, 6, 1, 1, 1, 1, 1, 6, 6, 6, 15, 15, 15, 15, 15, 1, 1, 1, 1, 22, 22, 22, 22, 1, 1, 6, 15, 3, 1, 1] 96 rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 19, 20, 21, 22, 27, 28] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 29, 30, 31]) total number of confs: 83 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042836 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042836 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042836/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042836 Building REAL250005042837 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042837' /scratch/stefan/7921153/working/building/REAL250005042837 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042837 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042837/0 /scratch/stefan/7921153/working/building/REAL250005042837 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 948) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/948 `/scratch/stefan/7921153/working/3D/948' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CO)C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1) `REAL250005042837.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042837/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:2-3 Rotatable hydrogens reported. Reducing confs by a factor of 3 WARNING:root:Setting energy window to 12 and max confs to 66 ('energy: ', 12.0) ('conf: ', 66) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042837 none CC(CO)C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 252 conformations in input total number of sets (complete confs): 252 using faster count positions algorithm for large data unique positions, atoms: [25, 17, 25, 28, 11, 17, 11, 11, 5, 11, 5, 1, 5, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 25, 25, 25, 25, 28, 28, 84, 11, 11, 5, 1, 33, 11, 11] 252 rigid atoms, others: [33, 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, 34, 35, 36]) total number of confs: 230 number of broken/clashed sets: 57 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042837 none CC(CO)C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 252 conformations in input total number of sets (complete confs): 252 using faster count positions algorithm for large data unique positions, atoms: [10, 5, 10, 20, 1, 5, 1, 1, 1, 1, 1, 6, 6, 6, 11, 11, 11, 11, 11, 1, 1, 1, 1, 10, 10, 10, 10, 20, 20, 60, 1, 1, 6, 11, 6, 1, 1] 252 rigid atoms, others: [35, 4, 6, 7, 8, 9, 10, 19, 20, 21, 22, 36, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34]) total number of confs: 175 number of broken/clashed sets: 57 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042837 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042837 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042837/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042837 Building REAL250005042838 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042838' /scratch/stefan/7921153/working/building/REAL250005042838 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042838 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042838/0 /scratch/stefan/7921153/working/building/REAL250005042838 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 949) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/949 `/scratch/stefan/7921153/working/3D/949' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CN(C(=O)C2(O)CC2)C[C@@H]1O)C1=CC(=O)[N-]O1) `REAL250005042838.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042838/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:2-3 Rotatable hydrogens reported. Reducing confs by a factor of 3 WARNING:root:Setting energy window to 12 and max confs to 66 ('energy: ', 12.0) ('conf: ', 66) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042838 none O=C(N[C@@H]1CN(C(=O)C2(O)CC2)C[C@@H]1O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 12, 1, 1, 1, 11, 8, 12, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 216 conformations in input total number of sets (complete confs): 216 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 12, 12, 12, 12, 20, 20, 24, 24, 24, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 8, 12, 12, 72, 24, 24, 24, 24, 12, 12, 36, 1] 216 rigid atoms, others: [1, 34, 17, 18, 19, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 179 number of broken/clashed sets: 51 ./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: REAL250005042838 none O=C(N[C@@H]1CN(C(=O)C2(O)CC2)C[C@@H]1O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 12, 1, 1, 1, 11, 8, 12, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 216 conformations in input total number of sets (complete confs): 216 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 15, 15, 15, 15, 8, 1, 8, 1, 1, 1, 1, 15, 15, 15, 15, 22, 24, 24, 24, 24, 24, 22, 15, 15, 6, 1, 1, 1, 1, 15, 15, 45, 24] 216 rigid atoms, others: [7, 9, 10, 11, 12, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34]) total number of confs: 110 number of broken/clashed sets: 51 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042838 none O=C(N[C@@H]1CN(C(=O)C2(O)CC2)C[C@@H]1O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 12, 1, 1, 1, 11, 8, 12, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 216 conformations in input total number of sets (complete confs): 216 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 1, 1, 1, 1, 1, 1, 6, 6, 15, 15, 15, 1, 1, 1, 1, 5, 12, 12, 12, 12, 12, 5, 1, 1, 45, 15, 15, 15, 15, 1, 1, 6, 12] 216 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 24, 25, 31] set([0, 1, 34, 33, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30]) total number of confs: 110 number of broken/clashed sets: 51 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042838 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042838 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042838/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042838 Building REAL250005042839 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042839' /scratch/stefan/7921153/working/building/REAL250005042839 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042839 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042839/0 /scratch/stefan/7921153/working/building/REAL250005042839 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 950) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/950 `/scratch/stefan/7921153/working/3D/950' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CN(C(=O)C2=CCC2)C[C@@H]1O)C1=CC(=O)[N-]O1) `REAL250005042839.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042839.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042839/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042839 none O=C(N[C@@H]1CN(C(=O)C2=CCC2)C[C@@H]1O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 7, 12, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 84 conformations in input total number of sets (complete confs): 84 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 14, 14, 14, 14, 28, 28, 28, 28, 28, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 9, 14, 14, 28, 28, 28, 28, 28, 14, 14, 42, 1] 84 rigid atoms, others: [1, 34, 17, 18, 19, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 119 number of broken/clashed sets: 10 ./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: REAL250005042839 none O=C(N[C@@H]1CN(C(=O)C2=CCC2)C[C@@H]1O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 7, 12, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 84 conformations in input total number of sets (complete confs): 84 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 17, 17, 17, 17, 9, 1, 9, 1, 1, 1, 1, 17, 17, 17, 17, 25, 28, 28, 28, 28, 28, 25, 17, 17, 1, 1, 1, 1, 1, 17, 17, 51, 28] 84 rigid atoms, others: [7, 9, 10, 11, 12, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 31, 32, 33, 34]) total number of confs: 120 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042839 none O=C(N[C@@H]1CN(C(=O)C2=CCC2)C[C@@H]1O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 7, 12, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 84 conformations in input total number of sets (complete confs): 84 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 17, 17, 17, 1, 1, 1, 1, 5, 14, 14, 14, 14, 14, 5, 1, 1, 17, 17, 17, 17, 17, 1, 1, 6, 14] 84 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 24, 25, 31] set([0, 1, 34, 33, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30]) total number of confs: 58 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042839 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042839 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042839/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042839 Building REAL250005042840 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042840' /scratch/stefan/7921153/working/building/REAL250005042840 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042840 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042840/0 /scratch/stefan/7921153/working/building/REAL250005042840 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 951) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/951 `/scratch/stefan/7921153/working/3D/951' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=CC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1) `REAL250005042840.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042840.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042840/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042840 none CC=CC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [25, 25, 20, 14, 20, 14, 14, 8, 14, 8, 1, 8, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 25, 25, 25, 25, 25, 14, 14, 8, 1, 42, 14, 14] 75 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33]) total number of confs: 119 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042840 none CC=CC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [15, 15, 7, 1, 7, 1, 1, 1, 1, 1, 5, 5, 5, 14, 14, 14, 14, 14, 1, 1, 1, 1, 15, 15, 15, 15, 15, 1, 1, 5, 14, 3, 1, 1] 75 rigid atoms, others: [32, 33, 3, 5, 6, 7, 8, 9, 18, 19, 20, 21, 27, 28] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 29, 30, 31]) total number of confs: 63 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042840 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042840 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042840/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042840 Building REAL250005042841 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042841' /scratch/stefan/7921153/working/building/REAL250005042841 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042841 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042841/0 /scratch/stefan/7921153/working/building/REAL250005042841 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 952) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/952 `/scratch/stefan/7921153/working/3D/952' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(C=CCF)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1) `REAL250005042841.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042841.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042841/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042841 none O=C(C=CCF)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 1, 1, 5, 15, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [23, 16, 23, 33, 33, 35, 16, 16, 8, 16, 8, 1, 8, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 33, 33, 35, 35, 16, 16, 8, 1, 48, 16, 16] 105 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33]) total number of confs: 155 number of broken/clashed sets: 26 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042841 none O=C(C=CCF)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 1, 1, 5, 15, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 12, 13, 25, 1, 1, 1, 1, 1, 6, 6, 6, 16, 16, 16, 16, 16, 1, 1, 1, 1, 12, 12, 25, 25, 1, 1, 6, 16, 3, 1, 1] 105 rigid atoms, others: [32, 1, 33, 6, 7, 8, 9, 10, 19, 20, 21, 22, 27, 28] set([0, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 29, 30, 31]) total number of confs: 118 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042841 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042841 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042841/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042841 Building REAL250005042842 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042842' /scratch/stefan/7921153/working/building/REAL250005042842 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types Protomer extracton resulted in 0 protomers Marking REAL250005042842 as failed and skipping /scratch/stefan/7921153/working /scratch/stefan/7921153 `/scratch/stefan/7921153/working/building/REAL250005042842' -> `/scratch/stefan/7921153/failed/REAL250005042842' Building REAL250005042843 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042843' /scratch/stefan/7921153/working/building/REAL250005042843 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042843 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042843/0 /scratch/stefan/7921153/working/building/REAL250005042843 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 953) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/953 `/scratch/stefan/7921153/working/3D/953' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](O)C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1) `REAL250005042843.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042843/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:2-3 Rotatable hydrogens reported. Reducing confs by a factor of 3 WARNING:root:Setting energy window to 12 and max confs to 66 ('energy: ', 12.0) ('conf: ', 66) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042843 none C[C@H](O)C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 7, 7, 7, 6, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 225 conformations in input total number of sets (complete confs): 225 using faster count positions algorithm for large data unique positions, atoms: [25, 17, 25, 25, 11, 17, 11, 11, 7, 11, 7, 1, 7, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 25, 25, 25, 75, 11, 11, 7, 1, 33, 11, 11] 225 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33]) total number of confs: 199 number of broken/clashed sets: 80 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042843 none C[C@H](O)C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 7, 7, 7, 6, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 225 conformations in input total number of sets (complete confs): 225 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 13, 13, 1, 5, 1, 1, 1, 1, 1, 6, 6, 6, 11, 11, 11, 11, 11, 1, 1, 1, 1, 13, 13, 13, 39, 1, 1, 6, 11, 6, 1, 1] 225 rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 19, 20, 21, 22, 27, 28] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 29, 30, 31]) total number of confs: 107 number of broken/clashed sets: 80 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042843 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042843 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042843/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042843 Building REAL250005042844 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042844' /scratch/stefan/7921153/working/building/REAL250005042844 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042844 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042844/0 /scratch/stefan/7921153/working/building/REAL250005042844 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 954) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/954 `/scratch/stefan/7921153/working/3D/954' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CON=CC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1) `REAL250005042844.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042844.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042844/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042844 none CON=CC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 8, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 165 conformations in input total number of sets (complete confs): 165 using faster count positions algorithm for large data unique positions, atoms: [55, 55, 55, 29, 15, 29, 15, 15, 9, 15, 9, 1, 9, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 55, 55, 55, 55, 15, 15, 9, 1, 45, 15, 15] 165 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33]) total number of confs: 198 number of broken/clashed sets: 34 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042844 none CON=CC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 8, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 165 conformations in input total number of sets (complete confs): 165 using faster count positions algorithm for large data unique positions, atoms: [33, 26, 26, 7, 1, 6, 1, 1, 1, 1, 1, 6, 6, 6, 15, 15, 15, 15, 15, 1, 1, 1, 1, 33, 33, 33, 26, 1, 1, 6, 15, 3, 1, 1] 165 rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 19, 20, 21, 22, 27, 28] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 29, 30, 31]) total number of confs: 101 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042844 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042844 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042844/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042844 Building REAL250005042845 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042845' /scratch/stefan/7921153/working/building/REAL250005042845 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042845 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042845/0 /scratch/stefan/7921153/working/building/REAL250005042845 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 955) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/955 `/scratch/stefan/7921153/working/3D/955' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H]1C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1) `REAL250005042845.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042845/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042845 none C[C@@H]1C[C@H]1C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [37, 37, 37, 37, 31, 37, 18, 31, 18, 18, 8, 18, 8, 1, 8, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 37, 37, 37, 37, 37, 18, 18, 8, 1, 54, 18, 18] 111 rigid atoms, others: [33, 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, 34, 35, 36]) total number of confs: 165 number of broken/clashed sets: 17 ./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: REAL250005042845 none C[C@@H]1C[C@H]1C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 21, 21, 7, 21, 1, 7, 1, 1, 1, 1, 1, 5, 5, 5, 18, 18, 18, 18, 18, 1, 1, 1, 1, 21, 21, 21, 21, 21, 1, 1, 5, 18, 3, 1, 1] 111 rigid atoms, others: [35, 36, 6, 8, 9, 10, 11, 12, 21, 22, 23, 24, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 32, 33, 34]) total number of confs: 83 number of broken/clashed sets: 17 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042845 none C[C@@H]1C[C@H]1C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 8, 8, 21, 21, 21, 21, 32, 32, 32, 37, 37, 37, 37, 37, 21, 21, 21, 21, 2, 2, 2, 1, 1, 21, 21, 32, 37, 63, 21, 21] 111 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 156 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042845 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042845 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042845/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042845 Building REAL250005042846 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042846' /scratch/stefan/7921153/working/building/REAL250005042846 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042846 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042846/0 /scratch/stefan/7921153/working/building/REAL250005042846 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 956) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/956 `/scratch/stefan/7921153/working/3D/956' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(O)C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1) `REAL250005042846.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042846/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:2-3 Rotatable hydrogens reported. Reducing confs by a factor of 3 WARNING:root:Setting energy window to 12 and max confs to 66 ('energy: ', 12.0) ('conf: ', 66) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042846 none CC(C)(O)C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 297 conformations in input total number of sets (complete confs): 297 using faster count positions algorithm for large data unique positions, atoms: [33, 24, 33, 33, 10, 24, 10, 10, 6, 10, 6, 1, 6, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 33, 33, 33, 33, 33, 33, 99, 10, 10, 6, 1, 30, 10, 10] 297 rigid atoms, others: [33, 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, 34, 35, 36]) total number of confs: 250 number of broken/clashed sets: 125 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042846 none CC(C)(O)C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 297 conformations in input total number of sets (complete confs): 297 using faster count positions algorithm for large data unique positions, atoms: [13, 7, 13, 13, 1, 7, 1, 1, 1, 1, 1, 5, 5, 5, 10, 10, 10, 10, 10, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 39, 1, 1, 5, 10, 3, 1, 1] 297 rigid atoms, others: [35, 4, 6, 7, 8, 9, 10, 19, 20, 21, 22, 36, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34]) total number of confs: 112 number of broken/clashed sets: 125 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042846 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042846 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042846/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042846 Building REAL250005042847 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042847' /scratch/stefan/7921153/working/building/REAL250005042847 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042847 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042847/0 /scratch/stefan/7921153/working/building/REAL250005042847 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 957) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/957 `/scratch/stefan/7921153/working/3D/957' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C(C)CC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1) `REAL250005042847.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042847/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042847 none C=C(C)CC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [64, 63, 64, 36, 16, 36, 16, 16, 7, 16, 7, 1, 7, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 64, 64, 64, 64, 64, 63, 63, 16, 16, 8, 1, 48, 16, 16] 192 rigid atoms, others: [33, 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, 34, 35, 36]) total number of confs: 269 number of broken/clashed sets: 40 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042847 none C=C(C)CC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [40, 28, 40, 6, 1, 6, 1, 1, 1, 1, 1, 6, 6, 6, 16, 16, 16, 16, 16, 1, 1, 1, 1, 40, 40, 40, 40, 40, 29, 29, 1, 1, 6, 16, 3, 1, 1] 192 rigid atoms, others: [35, 4, 6, 7, 8, 9, 10, 19, 20, 21, 22, 36, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34]) total number of confs: 168 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042847 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042847 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042847/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042847 Building REAL250005042848 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042848' /scratch/stefan/7921153/working/building/REAL250005042848 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042848 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042848/0 /scratch/stefan/7921153/working/building/REAL250005042848 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 958) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/958 `/scratch/stefan/7921153/working/3D/958' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1) `REAL250005042848.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042848/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042848 none C=CCC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [64, 64, 40, 20, 40, 20, 20, 9, 20, 9, 1, 9, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 64, 64, 64, 64, 64, 20, 20, 10, 1, 60, 20, 20] 192 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33]) total number of confs: 284 number of broken/clashed sets: 38 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042848 none C=CCC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [43, 24, 6, 1, 6, 1, 1, 1, 1, 1, 6, 6, 6, 20, 20, 20, 20, 20, 1, 1, 1, 1, 43, 43, 43, 24, 24, 1, 1, 6, 20, 3, 1, 1] 192 rigid atoms, others: [32, 33, 3, 5, 6, 7, 8, 9, 18, 19, 20, 21, 27, 28] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 29, 30, 31]) total number of confs: 178 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042848 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042848 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042848/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042848 Building REAL250005042849 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042849' /scratch/stefan/7921153/working/building/REAL250005042849 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005042849 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042849/0 /scratch/stefan/7921153/working/building/REAL250005042849 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 959) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/959 `/scratch/stefan/7921153/working/3D/959' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[NH+](C)CC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1) `REAL250005042849.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042849.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042849/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042849 none C[NH+](C)CC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [26, 26, 26, 26, 18, 14, 18, 14, 14, 9, 14, 9, 1, 9, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 26, 26, 26, 26, 26, 26, 26, 26, 14, 14, 10, 1, 42, 14, 14] 78 rigid atoms, others: [35, 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, 36, 37, 38]) total number of confs: 136 number of broken/clashed sets: 22 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042849 none C[NH+](C)CC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [16, 16, 16, 16, 4, 1, 4, 1, 1, 1, 1, 1, 5, 5, 5, 14, 14, 14, 14, 13, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1, 5, 14, 3, 1, 1] 78 rigid atoms, others: [32, 33, 5, 38, 7, 8, 9, 10, 11, 20, 21, 22, 23, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36]) total number of confs: 83 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042849 /scratch/stefan/7921153/working /scratch/stefan/7921153 mkdir: created directory `1' /scratch/stefan/7921153/working/building/REAL250005042849/1 /scratch/stefan/7921153/working/building/REAL250005042849 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 1 (index: 960) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/960 `/scratch/stefan/7921153/working/3D/960' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1) `REAL250005042849.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005042849.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042849/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042849 none CN(C)CC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [56, 54, 56, 26, 11, 26, 11, 11, 5, 11, 5, 1, 5, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 56, 56, 56, 56, 56, 56, 54, 54, 11, 11, 6, 1, 33, 11, 11] 168 rigid atoms, others: [34, 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, 35, 36, 37]) total number of confs: 230 number of broken/clashed sets: 29 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042849 none CN(C)CC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [36, 26, 36, 6, 1, 6, 1, 1, 1, 1, 1, 6, 6, 6, 11, 11, 11, 11, 10, 1, 1, 1, 1, 36, 36, 36, 36, 36, 36, 26, 26, 1, 1, 6, 11, 3, 1, 1] 168 rigid atoms, others: [32, 4, 37, 6, 7, 8, 9, 10, 19, 20, 21, 22, 36, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35]) total number of confs: 153 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042849 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042849 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 1: /scratch/stefan/7921153/working/building/REAL250005042849/1.* 0: /scratch/stefan/7921153/working/building/REAL250005042849/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042849 Building REAL250005042850 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042850' /scratch/stefan/7921153/working/building/REAL250005042850 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042850 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042850/0 /scratch/stefan/7921153/working/building/REAL250005042850 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 961) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/961 `/scratch/stefan/7921153/working/3D/961' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CCC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1) `REAL250005042850.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042850.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042850/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042850 none N#CCC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [38, 38, 21, 14, 21, 14, 14, 7, 14, 7, 1, 7, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 38, 38, 14, 14, 8, 1, 42, 14, 14] 114 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30]) total number of confs: 184 number of broken/clashed sets: 23 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042850 none N#CCC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [18, 18, 4, 1, 4, 1, 1, 1, 1, 1, 6, 6, 6, 14, 14, 14, 14, 14, 1, 1, 1, 1, 19, 19, 1, 1, 6, 14, 3, 1, 1] 114 rigid atoms, others: [3, 5, 6, 7, 8, 9, 18, 19, 20, 21, 24, 25, 29, 30] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 26, 27, 28]) total number of confs: 85 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042850 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042850 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042850/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042850 Building REAL250005042851 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042851' /scratch/stefan/7921153/working/building/REAL250005042851 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042851 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042851/0 /scratch/stefan/7921153/working/building/REAL250005042851 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 962) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/962 `/scratch/stefan/7921153/working/3D/962' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CN(C(=O)C2CC2F)C[C@@H]1O)C1=CC(=O)[N-]O1) `REAL250005042851.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042851/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042851 none O=C(N[C@@H]1CN(C(=O)C2CC2F)C[C@@H]1O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 15, 5, 5, 7, 12, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 138 conformations in input total number of sets (complete confs): 138 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 10, 18, 18, 18, 18, 36, 36, 46, 46, 46, 18, 18, 18, 18, 1, 1, 1, 1, 1, 1, 10, 18, 18, 46, 46, 46, 46, 18, 18, 54, 1] 138 rigid atoms, others: [1, 33, 17, 18, 19, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 197 number of broken/clashed sets: 17 ./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: REAL250005042851 none O=C(N[C@@H]1CN(C(=O)C2CC2F)C[C@@H]1O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 15, 5, 5, 7, 12, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 138 conformations in input total number of sets (complete confs): 138 using faster count positions algorithm for large data unique positions, atoms: [38, 38, 23, 23, 23, 23, 8, 1, 8, 1, 1, 1, 1, 23, 23, 23, 23, 38, 46, 46, 46, 46, 46, 38, 23, 23, 1, 1, 1, 1, 23, 23, 69, 46] 138 rigid atoms, others: [7, 9, 10, 11, 12, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33]) total number of confs: 172 number of broken/clashed sets: 17 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042851 none O=C(N[C@@H]1CN(C(=O)C2CC2F)C[C@@H]1O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 15, 5, 5, 7, 12, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 138 conformations in input total number of sets (complete confs): 138 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 23, 23, 23, 1, 1, 1, 1, 5, 18, 18, 18, 18, 18, 5, 1, 1, 23, 23, 23, 23, 1, 1, 6, 18] 138 rigid atoms, others: [2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 24, 25, 30, 31] set([0, 1, 33, 32, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29]) total number of confs: 92 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042851 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042851 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042851/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042851 Building REAL250005042852 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042852' /scratch/stefan/7921153/working/building/REAL250005042852 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042852 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042852/0 /scratch/stefan/7921153/working/building/REAL250005042852 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 963) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/963 `/scratch/stefan/7921153/working/3D/963' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCF)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1) `REAL250005042852.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042852.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042852/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042852 none O=C(CCF)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'F', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 15, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 156 conformations in input total number of sets (complete confs): 156 using faster count positions algorithm for large data unique positions, atoms: [25, 15, 25, 52, 52, 15, 15, 7, 15, 7, 1, 7, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 52, 52, 52, 52, 15, 15, 8, 1, 45, 15, 15] 156 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32]) total number of confs: 235 number of broken/clashed sets: 31 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042852 none O=C(CCF)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'F', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 15, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 156 conformations in input total number of sets (complete confs): 156 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 15, 27, 1, 1, 1, 1, 1, 6, 6, 6, 15, 15, 15, 15, 15, 1, 1, 1, 1, 16, 16, 26, 26, 1, 1, 6, 15, 3, 1, 1] 156 rigid atoms, others: [32, 1, 5, 6, 7, 8, 9, 18, 19, 20, 21, 26, 27, 31] set([0, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 28, 29, 30]) total number of confs: 140 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042852 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042852 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042852/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042852 Building REAL250005042853 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042853' /scratch/stefan/7921153/working/building/REAL250005042853 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042853 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042853/0 /scratch/stefan/7921153/working/building/REAL250005042853 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 964) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/964 `/scratch/stefan/7921153/working/3D/964' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H](C)C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1) `REAL250005042853.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042853.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042853/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042853 none CO[C@H](C)C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 23, 33, 33, 10, 23, 10, 10, 5, 10, 5, 1, 5, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 33, 33, 33, 33, 33, 33, 10, 10, 5, 1, 30, 10, 10] 99 rigid atoms, others: [33, 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, 34, 35, 36]) total number of confs: 147 number of broken/clashed sets: 12 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042853 none CO[C@H](C)C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [21, 17, 6, 17, 17, 1, 6, 1, 1, 1, 1, 1, 5, 5, 5, 10, 10, 10, 10, 10, 1, 1, 1, 1, 21, 21, 21, 17, 17, 17, 1, 1, 5, 10, 3, 1, 1] 99 rigid atoms, others: [35, 36, 5, 7, 8, 9, 10, 11, 20, 21, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 32, 33, 34]) total number of confs: 90 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042853 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042853 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042853/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042853 Building REAL250005042854 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042854' /scratch/stefan/7921153/working/building/REAL250005042854 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042854 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042854/0 /scratch/stefan/7921153/working/building/REAL250005042854 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 965) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/965 `/scratch/stefan/7921153/working/3D/965' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](O)C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1) `REAL250005042854.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042854/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:2-3 Rotatable hydrogens reported. Reducing confs by a factor of 3 WARNING:root:Setting energy window to 12 and max confs to 66 ('energy: ', 12.0) ('conf: ', 66) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042854 none C[C@@H](O)C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 7, 7, 7, 6, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 225 conformations in input total number of sets (complete confs): 225 using faster count positions algorithm for large data unique positions, atoms: [25, 17, 25, 25, 10, 17, 10, 10, 6, 10, 6, 1, 6, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 25, 25, 25, 75, 10, 10, 6, 1, 30, 10, 10] 225 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33]) total number of confs: 191 number of broken/clashed sets: 69 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042854 none C[C@@H](O)C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 7, 7, 7, 6, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 225 conformations in input total number of sets (complete confs): 225 using faster count positions algorithm for large data unique positions, atoms: [14, 6, 14, 14, 1, 6, 1, 1, 1, 1, 1, 6, 6, 6, 10, 10, 10, 10, 10, 1, 1, 1, 1, 14, 14, 14, 42, 1, 1, 6, 10, 6, 1, 1] 225 rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 19, 20, 21, 22, 27, 28] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 29, 30, 31]) total number of confs: 113 number of broken/clashed sets: 69 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042854 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042854 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042854/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042854 Building REAL250005042855 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042855' /scratch/stefan/7921153/working/building/REAL250005042855 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042855 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042855/0 /scratch/stefan/7921153/working/building/REAL250005042855 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 966) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/966 `/scratch/stefan/7921153/working/3D/966' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C1CC1C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1) `REAL250005042855.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042855.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042855/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042855 none C=C1CC1C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 30, 16, 11, 16, 11, 11, 8, 11, 8, 1, 8, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 30, 30, 30, 30, 30, 11, 11, 8, 1, 33, 11, 11] 90 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 31] 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, 32, 33, 34]) total number of confs: 124 number of broken/clashed sets: 21 ./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: REAL250005042855 none C=C1CC1C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [15, 15, 15, 4, 1, 4, 1, 1, 1, 1, 1, 5, 5, 5, 11, 11, 11, 11, 11, 1, 1, 1, 1, 15, 15, 15, 15, 15, 1, 1, 5, 11, 3, 1, 1] 90 rigid atoms, others: [33, 34, 4, 6, 7, 8, 9, 10, 19, 20, 21, 22, 28, 29] set([0, 1, 2, 3, 5, 32, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 30, 31]) total number of confs: 59 number of broken/clashed sets: 21 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042855 none C=C1CC1C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 8, 8, 15, 15, 15, 15, 25, 25, 25, 30, 30, 30, 30, 30, 15, 15, 15, 15, 1, 1, 1, 1, 1, 15, 15, 25, 30, 45, 15, 15] 90 rigid atoms, others: [0, 1, 2, 3, 4, 23, 24, 25, 26, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 120 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042855 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042855 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042855/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042855 Building REAL250005042856 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042856' /scratch/stefan/7921153/working/building/REAL250005042856 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042856 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042856/0 /scratch/stefan/7921153/working/building/REAL250005042856 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 967) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/967 `/scratch/stefan/7921153/working/3D/967' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC1C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1) `REAL250005042856.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042856/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042856 none CC1=CC1C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [40, 40, 40, 31, 17, 31, 17, 17, 10, 17, 10, 1, 10, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 40, 40, 40, 40, 40, 17, 17, 10, 1, 51, 17, 17] 120 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 31] 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, 32, 33, 34]) total number of confs: 166 number of broken/clashed sets: 14 ./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: REAL250005042856 none CC1=CC1C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 22, 6, 1, 6, 1, 1, 1, 1, 1, 5, 5, 5, 17, 17, 17, 17, 17, 1, 1, 1, 1, 22, 22, 22, 22, 22, 1, 1, 5, 17, 6, 1, 1] 120 rigid atoms, others: [33, 34, 4, 6, 7, 8, 9, 10, 19, 20, 21, 22, 28, 29] set([0, 1, 2, 3, 5, 32, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 30, 31]) total number of confs: 87 number of broken/clashed sets: 14 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042856 none CC1=CC1C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 9, 9, 22, 22, 22, 22, 35, 35, 35, 40, 40, 40, 40, 40, 22, 22, 22, 22, 2, 2, 2, 1, 1, 22, 22, 35, 40, 66, 22, 22] 120 rigid atoms, others: [0, 1, 2, 3, 4, 26, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 167 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042856 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042856 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042856/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042856 Building REAL250005042857 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042857' /scratch/stefan/7921153/working/building/REAL250005042857 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042857 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042857/0 /scratch/stefan/7921153/working/building/REAL250005042857 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 968) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/968 `/scratch/stefan/7921153/working/3D/968' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1) `REAL250005042857.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042857/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042857 none C=CC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 11, 17, 11, 11, 6, 11, 6, 1, 6, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 17, 17, 17, 11, 11, 6, 1, 33, 11, 11] 51 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30]) total number of confs: 80 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042857 none C=CC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 12, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [11, 5, 1, 5, 1, 1, 1, 1, 1, 6, 6, 6, 11, 11, 11, 11, 11, 1, 1, 1, 1, 11, 11, 11, 1, 1, 6, 11, 6, 1, 1] 51 rigid atoms, others: [2, 4, 5, 6, 7, 8, 17, 18, 19, 20, 24, 25, 29, 30] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 26, 27, 28]) total number of confs: 53 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042857 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042857 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042857/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042857 Building REAL250005042858 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042858' /scratch/stefan/7921153/working/building/REAL250005042858 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042858 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042858/0 /scratch/stefan/7921153/working/building/REAL250005042858 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 969) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/969 `/scratch/stefan/7921153/working/3D/969' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N1CC[C@H]2CCN(C(=O)C3=CC(=O)[N-]O3)[C@H]2C1) `REAL250005042858.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042858.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042858/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042858 none CCC(=O)N1CC[C@H]2CCN(C(=O)C3=CC(=O)[N-]O3)[C@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 15, 26, 15, 15, 14, 14, 15, 15, 15, 8, 1, 8, 1, 1, 1, 1, 1, 1, 14, 14, 15, 26, 26, 26, 26, 26, 15, 15, 15, 14, 15, 15, 15, 15, 1, 15, 15] 26 rigid atoms, others: [36, 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, 37, 38]) total number of confs: 71 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042858 none CCC(=O)N1CC[C@H]2CCN(C(=O)C3=CC(=O)[N-]O3)[C@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [8, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 14, 15, 15, 15, 15, 1, 1, 1, 9, 9, 9, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 14, 1, 1] 26 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38] set([0, 1, 3, 36, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042858 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042858 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042858/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042858 Building REAL250005042859 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042859' /scratch/stefan/7921153/working/building/REAL250005042859 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042859 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042859/0 /scratch/stefan/7921153/working/building/REAL250005042859 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 970) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/970 `/scratch/stefan/7921153/working/3D/970' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CC[C@H]2CCN(C(=O)C3=CC(=O)[N-]O3)[C@H]2C1) `REAL250005042859.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042859.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042859/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042859 none CC(=O)N1CC[C@H]2CCN(C(=O)C3=CC(=O)[N-]O3)[C@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 12, 13, 12, 12, 12, 12, 12, 12, 12, 7, 1, 7, 1, 1, 1, 1, 1, 1, 12, 12, 12, 13, 13, 13, 12, 12, 12, 12, 12, 12, 12, 12, 1, 12, 12] 13 rigid atoms, others: [33, 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, 34, 35]) total number of confs: 28 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042859 none CC(=O)N1CC[C@H]2CCN(C(=O)C3=CC(=O)[N-]O3)[C@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 12, 12, 12, 12, 12, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1] 13 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35] set([0, 33, 2, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24]) total number of confs: 32 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042859 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042859 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042859/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042859 Building REAL250005042860 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042860' /scratch/stefan/7921153/working/building/REAL250005042860 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042860 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042860/0 /scratch/stefan/7921153/working/building/REAL250005042860 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 971) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/971 `/scratch/stefan/7921153/working/3D/971' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CO)N1CC[C@H]2CCN(C(=O)C3=CC(=O)[N-]O3)[C@H]2C1) `REAL250005042860.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042860.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042860/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042860 none O=C(CO)N1CC[C@H]2CCN(C(=O)C3=CC(=O)[N-]O3)[C@H]2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [23, 16, 23, 23, 16, 16, 16, 16, 16, 16, 15, 8, 1, 8, 1, 1, 1, 1, 1, 1, 16, 16, 16, 23, 23, 69, 16, 16, 16, 16, 16, 16, 15, 15, 1, 15, 16] 69 rigid atoms, others: [34, 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, 35, 36]) total number of confs: 126 number of broken/clashed sets: 14 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042860 none O=C(CO)N1CC[C@H]2CCN(C(=O)C3=CC(=O)[N-]O3)[C@H]2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [5, 1, 5, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 16, 16, 16, 15, 15, 1, 1, 1, 13, 13, 39, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1] 69 rigid atoms, others: [1, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36] set([0, 2, 3, 13, 14, 15, 16, 17, 18, 19, 34, 23, 24, 25]) total number of confs: 110 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042860 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042860 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042860/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042860 Building REAL250005042861 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042861' /scratch/stefan/7921153/working/building/REAL250005042861 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042861 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042861/0 /scratch/stefan/7921153/working/building/REAL250005042861 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 972) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/972 `/scratch/stefan/7921153/working/3D/972' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N1CC[C@@H]2CCN(C(=O)C3=CC(=O)[N-]O3)C[C@@H]21) `REAL250005042861.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042861/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042861 none CCC(=O)N1CC[C@@H]2CCN(C(=O)C3=CC(=O)[N-]O3)C[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 18, 15, 18, 15, 15, 15, 15, 15, 15, 15, 9, 1, 9, 1, 1, 1, 1, 1, 1, 15, 15, 15, 20, 20, 20, 20, 20, 15, 15, 15, 15, 15, 15, 15, 15, 1, 15, 15] 20 rigid atoms, others: [36, 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, 37, 38]) total number of confs: 51 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042861 none CCC(=O)N1CC[C@@H]2CCN(C(=O)C3=CC(=O)[N-]O3)C[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 15, 15, 15, 15, 1, 1, 1, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1] 20 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38] set([0, 1, 3, 36, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27]) total number of confs: 55 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042861 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042861 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042861/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042861 Building REAL250005042862 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042862' /scratch/stefan/7921153/working/building/REAL250005042862 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042862 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042862/0 /scratch/stefan/7921153/working/building/REAL250005042862 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 973) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/973 `/scratch/stefan/7921153/working/3D/973' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CC[C@@H]2CCN(C(=O)C3=CC(=O)[N-]O3)C[C@@H]21) `REAL250005042862.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042862.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042862/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042862 none CC(=O)N1CC[C@@H]2CCN(C(=O)C3=CC(=O)[N-]O3)C[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 8, 1, 8, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 9, 9] 9 rigid atoms, others: [33, 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, 34, 35]) total number of confs: 19 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042862 none CC(=O)N1CC[C@@H]2CCN(C(=O)C3=CC(=O)[N-]O3)C[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 9, 9, 1, 1, 1, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 9, 1, 1] 9 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35] set([0, 33, 2, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24]) total number of confs: 25 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042862 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042862 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042862/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042862 Building REAL250005042863 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042863' /scratch/stefan/7921153/working/building/REAL250005042863 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042863 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042863/0 /scratch/stefan/7921153/working/building/REAL250005042863 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 974) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/974 `/scratch/stefan/7921153/working/3D/974' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CO)N1CC[C@@H]2CCN(C(=O)C3=CC(=O)[N-]O3)C[C@@H]21) `REAL250005042863.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042863.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042863/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042863 none O=C(CO)N1CC[C@@H]2CCN(C(=O)C3=CC(=O)[N-]O3)C[C@@H]21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 8, 1, 8, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 36, 12, 12, 12, 12, 12, 12, 12, 12, 1, 12, 12] 36 rigid atoms, others: [34, 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, 35, 36]) total number of confs: 60 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042863 none O=C(CO)N1CC[C@@H]2CCN(C(=O)C3=CC(=O)[N-]O3)C[C@@H]21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 12, 12, 12, 12, 12, 1, 1, 1, 5, 5, 15, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1] 36 rigid atoms, others: [1, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36] set([0, 2, 3, 13, 14, 15, 16, 17, 18, 19, 34, 23, 24, 25]) total number of confs: 52 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042863 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042863 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042863/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042863 Building REAL250005042864 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042864' /scratch/stefan/7921153/working/building/REAL250005042864 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042864 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042864/0 /scratch/stefan/7921153/working/building/REAL250005042864 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 975) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/975 `/scratch/stefan/7921153/working/3D/975' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(=O)N1CC[C@@H]2CCN(C(=O)C3=CC(=O)[N-]O3)C[C@@H]21) `REAL250005042864.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042864/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042864 none C=CC(=O)N1CC[C@@H]2CCN(C(=O)C3=CC(=O)[N-]O3)C[C@@H]21 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 24, 45, 24, 24, 24, 24, 24, 24, 24, 10, 1, 10, 1, 1, 1, 1, 1, 1, 24, 24, 24, 45, 45, 45, 24, 24, 24, 24, 24, 24, 24, 24, 1, 24, 24] 45 rigid atoms, others: [34, 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, 35, 36]) total number of confs: 109 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042864 none C=CC(=O)N1CC[C@@H]2CCN(C(=O)C3=CC(=O)[N-]O3)C[C@@H]21 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [17, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 24, 24, 24, 24, 24, 1, 1, 1, 17, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 24, 1, 1] 45 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36] set([0, 1, 34, 3, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042864 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042864 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042864/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042864 Building REAL250005042865 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042865' /scratch/stefan/7921153/working/building/REAL250005042865 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042865 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042865/0 /scratch/stefan/7921153/working/building/REAL250005042865 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 976) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/976 `/scratch/stefan/7921153/working/3D/976' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N[C@@H]1CCCC[C@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005042865.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042865/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042865 none CCC(=O)N[C@@H]1CCCC[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [31, 23, 23, 23, 16, 16, 16, 16, 16, 16, 16, 8, 16, 8, 1, 8, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31, 23, 16, 16, 16, 16, 16, 16, 16, 16, 9, 1] 31 rigid atoms, others: [37, 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]) total number of confs: 117 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042865 none CCC(=O)N[C@@H]1CCCC[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [17, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 16, 16, 16, 16, 16, 17, 17, 17, 17, 17, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 16] 31 rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 28, 29, 30, 31] set([0, 1, 2, 3, 36, 37, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042865 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042865 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042865/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042865 Building REAL250005042866 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042866' /scratch/stefan/7921153/working/building/REAL250005042866 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042866 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042866/0 /scratch/stefan/7921153/working/building/REAL250005042866 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 977) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/977 `/scratch/stefan/7921153/working/3D/977' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N[C@@H]1CCCC[C@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005042866.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042866.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042866/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042866 none CC(=O)N[C@@H]1CCCC[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 9, 9, 9, 9, 9, 9, 9, 5, 9, 5, 1, 5, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 9, 9, 9, 9, 9, 9, 9, 9, 5, 1] 13 rigid atoms, others: [34, 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]) total number of confs: 37 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042866 none CC(=O)N[C@@H]1CCCC[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 9, 9, 9, 9, 9, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9] 13 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 34, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 29 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042866 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042866 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042866/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042866 Building REAL250005042867 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042867' /scratch/stefan/7921153/working/building/REAL250005042867 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042867 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042867/0 /scratch/stefan/7921153/working/building/REAL250005042867 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 978) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/978 `/scratch/stefan/7921153/working/3D/978' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCCC[C@H]1NC(=O)C1CC1)C1=CC(=O)[N-]O1) `REAL250005042867.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042867.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042867/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042867 none O=C(N[C@@H]1CCCC[C@H]1NC(=O)C1CC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 7, 17, 17, 17, 17, 17, 17, 17, 17, 23, 23, 23, 37, 37, 1, 1, 1, 1, 1, 1, 7, 17, 17, 17, 17, 17, 17, 17, 17, 23, 37, 37, 37, 37, 37, 1] 37 rigid atoms, others: [1, 38, 17, 18, 19, 20, 21, 22] set([0, 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]) total number of confs: 117 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: REAL250005042867 none O=C(N[C@@H]1CCCC[C@H]1NC(=O)C1CC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [32, 32, 20, 20, 20, 20, 20, 20, 20, 9, 20, 9, 1, 9, 1, 1, 1, 32, 37, 37, 37, 37, 37, 32, 20, 20, 20, 20, 20, 20, 20, 20, 9, 1, 1, 1, 1, 1, 37] 37 rigid atoms, others: [33, 34, 35, 36, 37, 12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38]) total number of confs: 103 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042867 none O=C(N[C@@H]1CCCC[C@H]1NC(=O)C1CC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 20, 20, 6, 17, 17, 17, 17, 17, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 20, 20, 20, 20, 20, 17] 38 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 34, 35, 36, 33, 38, 32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 37]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042867 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042867 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042867/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042867 Building REAL250005042868 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042868' /scratch/stefan/7921153/working/building/REAL250005042868 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042868 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042868/0 /scratch/stefan/7921153/working/building/REAL250005042868 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 979) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/979 `/scratch/stefan/7921153/working/3D/979' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)N[C@@H]1CCCC[C@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005042868.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042868.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042868/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042868 none COCC(=O)N[C@@H]1CCCC[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [44, 44, 24, 24, 24, 17, 17, 17, 17, 17, 17, 17, 9, 17, 9, 1, 9, 1, 1, 1, 1, 1, 1, 44, 44, 44, 44, 44, 24, 17, 17, 17, 17, 17, 17, 17, 17, 9, 1] 44 rigid atoms, others: [38, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 159 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042868 none COCC(=O)N[C@@H]1CCCC[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [27, 20, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 17, 17, 17, 17, 17, 27, 27, 27, 20, 20, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 17] 44 rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 29, 30, 31] set([0, 1, 2, 3, 4, 37, 38, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042868 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042868 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042868/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042868 Building REAL250005042869 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042869' /scratch/stefan/7921153/working/building/REAL250005042869 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042869 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042869/0 /scratch/stefan/7921153/working/building/REAL250005042869 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 980) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/980 `/scratch/stefan/7921153/working/3D/980' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(=O)N[C@@H]1CCCC[C@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005042869.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042869.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042869/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042869 none CCCC(=O)N[C@@H]1CCCC[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [64, 63, 33, 33, 33, 21, 21, 21, 21, 21, 21, 21, 10, 21, 10, 1, 10, 1, 1, 1, 1, 1, 1, 64, 64, 64, 64, 64, 63, 63, 33, 21, 21, 21, 21, 21, 21, 21, 21, 10, 1] 64 rigid atoms, others: [40, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 243 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042869 none CCCC(=O)N[C@@H]1CCCC[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [35, 27, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 21, 21, 21, 21, 21, 37, 37, 37, 37, 37, 27, 27, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 21] 64 rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 38, 37, 31] set([0, 1, 2, 3, 4, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 39, 40]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042869 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042869 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042869/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042869 Building REAL250005042870 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042870' /scratch/stefan/7921153/working/building/REAL250005042870 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042870 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042870/0 /scratch/stefan/7921153/working/building/REAL250005042870 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 981) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/981 `/scratch/stefan/7921153/working/3D/981' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N[C@@H]1CCCC[C@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005042870.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042870.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042870/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042870 none CC(C)C(=O)N[C@@H]1CCCC[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [35, 28, 35, 28, 28, 19, 19, 19, 19, 19, 19, 19, 9, 19, 9, 1, 9, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 35, 35, 35, 28, 19, 19, 19, 19, 19, 19, 19, 19, 9, 1] 35 rigid atoms, others: [40, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 123 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042870 none CC(C)C(=O)N[C@@H]1CCCC[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [17, 6, 17, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 19, 19, 19, 19, 19, 17, 17, 17, 17, 17, 17, 17, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 19] 35 rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 38, 37, 31] set([0, 1, 2, 3, 4, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 39, 40]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042870 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042870 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042870/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042870 Building REAL250005042871 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042871' /scratch/stefan/7921153/working/building/REAL250005042871 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042871 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042871/0 /scratch/stefan/7921153/working/building/REAL250005042871 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 982) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/982 `/scratch/stefan/7921153/working/3D/982' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C(=O)N[C@@H]1CCCC[C@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005042871.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042871.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042871/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042871 none NC(=O)C(=O)N[C@@H]1CCCC[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [25, 24, 25, 24, 24, 16, 16, 16, 16, 16, 16, 16, 9, 16, 9, 1, 9, 1, 1, 1, 1, 1, 1, 25, 25, 24, 16, 16, 16, 16, 16, 16, 16, 16, 10, 1] 25 rigid atoms, others: [35, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 71 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042871 none NC(=O)C(=O)N[C@@H]1CCCC[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [15, 6, 15, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 16, 16, 16, 16, 16, 15, 15, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 16] 25 rigid atoms, others: [32, 33, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 35, 34, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042871 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042871 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042871/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042871 Building REAL250005042872 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042872' /scratch/stefan/7921153/working/building/REAL250005042872 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042872 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042872/0 /scratch/stefan/7921153/working/building/REAL250005042872 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 983) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/983 `/scratch/stefan/7921153/working/3D/983' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC(=O)N[C@@H]1CCCC[C@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005042872.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042872.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042872/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042872 none C=CCC(=O)N[C@@H]1CCCC[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 33, 33, 33, 20, 20, 20, 20, 20, 20, 20, 10, 20, 10, 1, 10, 1, 1, 1, 1, 1, 1, 49, 49, 49, 49, 49, 33, 20, 20, 20, 20, 20, 20, 20, 20, 11, 1] 49 rigid atoms, others: [38, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 177 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042872 none C=CCC(=O)N[C@@H]1CCCC[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [34, 25, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 20, 20, 20, 20, 20, 34, 34, 34, 25, 25, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 20] 49 rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 29, 30, 31] set([0, 1, 2, 3, 4, 37, 38, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042872 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042872 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042872/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042872 Building REAL250005042873 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042873' /scratch/stefan/7921153/working/building/REAL250005042873 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042873 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042873/0 /scratch/stefan/7921153/working/building/REAL250005042873 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 984) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/984 `/scratch/stefan/7921153/working/3D/984' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CO)N[C@@H]1CCCC[C@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005042873.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042873.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042873/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042873 none O=C(CO)N[C@@H]1CCCC[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [20, 20, 20, 23, 13, 13, 13, 13, 13, 13, 13, 6, 13, 6, 1, 6, 1, 1, 1, 1, 1, 1, 23, 23, 69, 20, 13, 13, 13, 13, 13, 13, 13, 13, 7, 1] 69 rigid atoms, others: [35, 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]) total number of confs: 148 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042873 none O=C(CO)N[C@@H]1CCCC[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [6, 6, 6, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 13, 13, 13, 13, 13, 15, 15, 45, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 13] 69 rigid atoms, others: [32, 33, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 35, 34, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042873 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042873 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042873/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042873 Building REAL250005042874 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042874' /scratch/stefan/7921153/working/building/REAL250005042874 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042874 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042874/0 /scratch/stefan/7921153/working/building/REAL250005042874 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 985) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/985 `/scratch/stefan/7921153/working/3D/985' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)C(=O)N[C@@H]1CCCC[C@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005042874.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042874.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042874/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042874 none CC(O)C(=O)N[C@@H]1CCCC[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [26, 20, 26, 20, 20, 12, 12, 12, 12, 12, 12, 12, 5, 12, 5, 1, 5, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 78, 20, 12, 12, 12, 12, 12, 12, 12, 12, 6, 1] 78 rigid atoms, others: [38, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 175 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042874 none CC(O)C(=O)N[C@@H]1CCCC[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [15, 6, 15, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 12, 12, 15, 15, 15, 15, 45, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 12] 78 rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 29, 30, 31] set([0, 1, 2, 3, 4, 37, 38, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042874 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042874 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042874/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042874 Building REAL250005042875 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042875' /scratch/stefan/7921153/working/building/REAL250005042875 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042875 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042875/0 /scratch/stefan/7921153/working/building/REAL250005042875 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 986) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/986 `/scratch/stefan/7921153/working/3D/986' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCF)N[C@@H]1CCCC[C@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005042875.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042875.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042875/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042875 none O=C(CCF)N[C@@H]1CCCC[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'F', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 15, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 33, 58, 58, 17, 17, 17, 17, 17, 17, 17, 10, 17, 10, 1, 10, 1, 1, 1, 1, 1, 1, 58, 58, 58, 58, 33, 17, 17, 17, 17, 17, 17, 17, 17, 10, 1] 58 rigid atoms, others: [37, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 203 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042875 none O=C(CCF)N[C@@H]1CCCC[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'F', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 15, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [6, 6, 6, 29, 41, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 17, 17, 17, 17, 17, 29, 29, 41, 41, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 17] 58 rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 37, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 36]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042875 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042875 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042875/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042875 Building REAL250005042876 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042876' /scratch/stefan/7921153/working/building/REAL250005042876 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042876 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042876/0 /scratch/stefan/7921153/working/building/REAL250005042876 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 987) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/987 `/scratch/stefan/7921153/working/3D/987' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](O)C(=O)N[C@@H]1CCCC[C@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005042876.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042876/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042876 none C[C@@H](O)C(=O)N[C@@H]1CCCC[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [33, 26, 33, 33, 26, 26, 16, 16, 16, 16, 16, 16, 16, 8, 16, 8, 1, 8, 1, 1, 1, 1, 1, 1, 33, 33, 33, 99, 26, 16, 16, 16, 16, 16, 16, 16, 16, 9, 1] 99 rigid atoms, others: [38, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 217 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042876 none C[C@@H](O)C(=O)N[C@@H]1CCCC[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [20, 6, 20, 20, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 16, 16, 16, 16, 16, 20, 20, 20, 60, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 16] 99 rigid atoms, others: [32, 33, 34, 35, 36, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 38, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 37]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042876 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042876 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042876/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042876 Building REAL250005042877 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042877' /scratch/stefan/7921153/working/building/REAL250005042877 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042877 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042877/0 /scratch/stefan/7921153/working/building/REAL250005042877 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 988) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/988 `/scratch/stefan/7921153/working/3D/988' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](O)C(=O)N[C@@H]1CCCC[C@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005042877.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042877.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042877/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042877 none C[C@H](O)C(=O)N[C@@H]1CCCC[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [26, 20, 26, 26, 20, 20, 12, 12, 12, 12, 12, 12, 12, 5, 12, 5, 1, 5, 1, 1, 1, 1, 1, 1, 26, 26, 26, 78, 20, 12, 12, 12, 12, 12, 12, 12, 12, 6, 1] 78 rigid atoms, others: [38, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 175 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042877 none C[C@H](O)C(=O)N[C@@H]1CCCC[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [15, 6, 15, 15, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 12, 12, 15, 15, 15, 45, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 12] 78 rigid atoms, others: [32, 33, 34, 35, 36, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 38, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 37]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042877 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042877 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042877/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042877 Building REAL250005042878 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042878' /scratch/stefan/7921153/working/building/REAL250005042878 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042878 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042878/0 /scratch/stefan/7921153/working/building/REAL250005042878 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 989) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/989 `/scratch/stefan/7921153/working/3D/989' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=CC(=O)N[C@@H]1CCCC[C@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005042878.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042878.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042878/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042878 none CC=CC(=O)N[C@@H]1CCCC[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 21, 21, 21, 15, 15, 15, 15, 15, 15, 15, 7, 15, 7, 1, 7, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 21, 15, 15, 15, 15, 15, 15, 15, 15, 8, 1] 29 rigid atoms, others: [38, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 93 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042878 none CC=CC(=O)N[C@@H]1CCCC[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 15, 15, 15, 15, 15, 16, 16, 16, 16, 16, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 15] 29 rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 29, 30, 31] set([0, 1, 2, 3, 4, 37, 38, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042878 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042878 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042878/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042878 Building REAL250005042879 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042879' /scratch/stefan/7921153/working/building/REAL250005042879 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042879 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042879/0 /scratch/stefan/7921153/working/building/REAL250005042879 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 990) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/990 `/scratch/stefan/7921153/working/3D/990' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)N[C@@H]1CCCC[C@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005042879.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042879.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042879/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042879 none COCC(=O)N[C@@H]1CCCC[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [44, 44, 24, 24, 24, 17, 17, 17, 17, 17, 17, 17, 9, 17, 9, 1, 9, 1, 1, 1, 1, 1, 1, 44, 44, 44, 44, 44, 24, 17, 17, 17, 17, 17, 17, 17, 17, 9, 1] 44 rigid atoms, others: [38, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 159 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042879 none COCC(=O)N[C@@H]1CCCC[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [27, 20, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 17, 17, 17, 17, 17, 27, 27, 27, 20, 20, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 17] 44 rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 29, 30, 31] set([0, 1, 2, 3, 4, 37, 38, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042879 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042879 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042879/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042879 Building REAL250005042880 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042880' /scratch/stefan/7921153/working/building/REAL250005042880 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042880 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042880/0 /scratch/stefan/7921153/working/building/REAL250005042880 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 991) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/991 `/scratch/stefan/7921153/working/3D/991' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(=O)N[C@@H]1CCCC[C@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005042880.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042880/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042880 none CCCC(=O)N[C@@H]1CCCC[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [64, 63, 33, 33, 33, 21, 21, 21, 21, 21, 21, 21, 10, 21, 10, 1, 10, 1, 1, 1, 1, 1, 1, 64, 64, 64, 64, 64, 63, 63, 33, 21, 21, 21, 21, 21, 21, 21, 21, 10, 1] 64 rigid atoms, others: [40, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 243 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042880 none CCCC(=O)N[C@@H]1CCCC[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [35, 27, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 21, 21, 21, 21, 21, 37, 37, 37, 37, 37, 27, 27, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 21] 64 rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 38, 37, 31] set([0, 1, 2, 3, 4, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 39, 40]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042880 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042880 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042880/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042880 Building REAL250005042881 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042881' /scratch/stefan/7921153/working/building/REAL250005042881 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042881 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042881/0 /scratch/stefan/7921153/working/building/REAL250005042881 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 992) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/992 `/scratch/stefan/7921153/working/3D/992' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N[C@@H]1CCCC[C@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005042881.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042881/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042881 none CC(C)C(=O)N[C@@H]1CCCC[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [35, 28, 35, 28, 28, 19, 19, 19, 19, 19, 19, 19, 9, 19, 9, 1, 9, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 35, 35, 35, 28, 19, 19, 19, 19, 19, 19, 19, 19, 9, 1] 35 rigid atoms, others: [40, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 123 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042881 none CC(C)C(=O)N[C@@H]1CCCC[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [17, 6, 17, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 19, 19, 19, 19, 19, 17, 17, 17, 17, 17, 17, 17, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 19] 35 rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 38, 37, 31] set([0, 1, 2, 3, 4, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 39, 40]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042881 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042881 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042881/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042881 Building REAL250005042882 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042882' /scratch/stefan/7921153/working/building/REAL250005042882 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042882 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042882/0 /scratch/stefan/7921153/working/building/REAL250005042882 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 993) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/993 `/scratch/stefan/7921153/working/3D/993' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N[C@@H]1CCCC[C@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005042882.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042882/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042882 none CCC(=O)N[C@@H]1CCCC[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [31, 23, 23, 23, 16, 16, 16, 16, 16, 16, 16, 8, 16, 8, 1, 8, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31, 23, 16, 16, 16, 16, 16, 16, 16, 16, 9, 1] 31 rigid atoms, others: [37, 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]) total number of confs: 117 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042882 none CCC(=O)N[C@@H]1CCCC[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [17, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 16, 16, 16, 16, 16, 17, 17, 17, 17, 17, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 16] 31 rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 28, 29, 30, 31] set([0, 1, 2, 3, 36, 37, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042882 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042882 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042882/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042882 Building REAL250005042883 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042883' /scratch/stefan/7921153/working/building/REAL250005042883 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042883 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042883/0 /scratch/stefan/7921153/working/building/REAL250005042883 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 994) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/994 `/scratch/stefan/7921153/working/3D/994' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N[C@@H]1CCCC[C@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005042883.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042883.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042883/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042883 none CC(=O)N[C@@H]1CCCC[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 9, 9, 9, 9, 9, 9, 9, 5, 9, 5, 1, 5, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 9, 9, 9, 9, 9, 9, 9, 9, 5, 1] 13 rigid atoms, others: [34, 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]) total number of confs: 37 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042883 none CC(=O)N[C@@H]1CCCC[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 9, 9, 9, 9, 9, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9] 13 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 34, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 29 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042883 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042883 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042883/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042883 Building REAL250005042884 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042884' /scratch/stefan/7921153/working/building/REAL250005042884 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042884 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042884/0 /scratch/stefan/7921153/working/building/REAL250005042884 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 995) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/995 `/scratch/stefan/7921153/working/3D/995' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCCC[C@H]1NC(=O)C1CC1)C1=CC(=O)[N-]O1) `REAL250005042884.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042884.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042884/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042884 none O=C(N[C@@H]1CCCC[C@H]1NC(=O)C1CC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 7, 17, 17, 17, 17, 17, 17, 17, 17, 23, 23, 23, 37, 37, 1, 1, 1, 1, 1, 1, 7, 17, 17, 17, 17, 17, 17, 17, 17, 23, 37, 37, 37, 37, 37, 1] 37 rigid atoms, others: [1, 38, 17, 18, 19, 20, 21, 22] set([0, 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]) total number of confs: 117 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: REAL250005042884 none O=C(N[C@@H]1CCCC[C@H]1NC(=O)C1CC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [32, 32, 20, 20, 20, 20, 20, 20, 20, 9, 20, 9, 1, 9, 1, 1, 1, 32, 37, 37, 37, 37, 37, 32, 20, 20, 20, 20, 20, 20, 20, 20, 9, 1, 1, 1, 1, 1, 37] 37 rigid atoms, others: [33, 34, 35, 36, 37, 12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38]) total number of confs: 103 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042884 none O=C(N[C@@H]1CCCC[C@H]1NC(=O)C1CC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 20, 20, 6, 17, 17, 17, 17, 17, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 20, 20, 20, 20, 20, 17] 38 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 34, 35, 36, 33, 38, 32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 37]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042884 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042884 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042884/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042884 Building REAL250005042885 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042885' /scratch/stefan/7921153/working/building/REAL250005042885 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042885 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042885/0 /scratch/stefan/7921153/working/building/REAL250005042885 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 996) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/996 `/scratch/stefan/7921153/working/3D/996' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C(=O)N[C@@H]1CCCC[C@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005042885.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042885.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042885/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042885 none NC(=O)C(=O)N[C@@H]1CCCC[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [25, 24, 25, 24, 24, 16, 16, 16, 16, 16, 16, 16, 9, 16, 9, 1, 9, 1, 1, 1, 1, 1, 1, 25, 25, 24, 16, 16, 16, 16, 16, 16, 16, 16, 10, 1] 25 rigid atoms, others: [35, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 71 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042885 none NC(=O)C(=O)N[C@@H]1CCCC[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [15, 6, 15, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 16, 16, 16, 16, 16, 15, 15, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 16] 25 rigid atoms, others: [32, 33, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 35, 34, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042885 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042885 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042885/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042885 Building REAL250005042886 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042886' /scratch/stefan/7921153/working/building/REAL250005042886 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042886 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042886/0 /scratch/stefan/7921153/working/building/REAL250005042886 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 997) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/997 `/scratch/stefan/7921153/working/3D/997' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CO)N[C@@H]1CCCC[C@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005042886.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042886/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042886 none O=C(CO)N[C@@H]1CCCC[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [20, 20, 20, 23, 13, 13, 13, 13, 13, 13, 13, 6, 13, 6, 1, 6, 1, 1, 1, 1, 1, 1, 23, 23, 69, 20, 13, 13, 13, 13, 13, 13, 13, 13, 7, 1] 69 rigid atoms, others: [35, 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]) total number of confs: 148 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042886 none O=C(CO)N[C@@H]1CCCC[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [6, 6, 6, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 13, 13, 13, 13, 13, 15, 15, 45, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 13] 69 rigid atoms, others: [32, 33, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 35, 34, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042886 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042886 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042886/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042886 Building REAL250005042887 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042887' /scratch/stefan/7921153/working/building/REAL250005042887 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042887 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042887/0 /scratch/stefan/7921153/working/building/REAL250005042887 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 998) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/998 `/scratch/stefan/7921153/working/3D/998' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)C(=O)N[C@@H]1CCCC[C@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005042887.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042887.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042887/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042887 none CC(O)C(=O)N[C@@H]1CCCC[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [26, 20, 26, 20, 20, 12, 12, 12, 12, 12, 12, 12, 5, 12, 5, 1, 5, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 78, 20, 12, 12, 12, 12, 12, 12, 12, 12, 6, 1] 78 rigid atoms, others: [38, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 175 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042887 none CC(O)C(=O)N[C@@H]1CCCC[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [15, 6, 15, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 12, 12, 15, 15, 15, 15, 45, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 12] 78 rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 29, 30, 31] set([0, 1, 2, 3, 4, 37, 38, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042887 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042887 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042887/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042887 Building REAL250005042888 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042888' /scratch/stefan/7921153/working/building/REAL250005042888 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042888 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042888/0 /scratch/stefan/7921153/working/building/REAL250005042888 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 999) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/999 `/scratch/stefan/7921153/working/3D/999' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)C(=O)N[C@@H]1CCCC[C@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005042888.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042888/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042888 none CC(=O)C(=O)N[C@@H]1CCCC[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [27, 23, 27, 23, 23, 13, 13, 13, 13, 13, 13, 13, 8, 13, 8, 1, 8, 1, 1, 1, 1, 1, 1, 27, 27, 27, 23, 13, 13, 13, 13, 13, 13, 13, 13, 8, 1] 27 rigid atoms, others: [36, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 79 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042888 none CC(=O)C(=O)N[C@@H]1CCCC[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [16, 6, 16, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 13, 13, 13, 13, 13, 16, 16, 16, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 13] 27 rigid atoms, others: [32, 33, 34, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 35, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36]) total number of confs: 64 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042888 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042888 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042888/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042888 Building REAL250005042889 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042889' /scratch/stefan/7921153/working/building/REAL250005042889 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042889 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042889/0 /scratch/stefan/7921153/working/building/REAL250005042889 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 1000) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/1000 `/scratch/stefan/7921153/working/3D/1000' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=CC(=O)N[C@@H]1CCCC[C@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005042889.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042889/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042889 none CC=CC(=O)N[C@@H]1CCCC[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 21, 21, 21, 15, 15, 15, 15, 15, 15, 15, 7, 15, 7, 1, 7, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 21, 15, 15, 15, 15, 15, 15, 15, 15, 8, 1] 29 rigid atoms, others: [38, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 93 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042889 none CC=CC(=O)N[C@@H]1CCCC[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 15, 15, 15, 15, 15, 16, 16, 16, 16, 16, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 15] 29 rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 29, 30, 31] set([0, 1, 2, 3, 4, 37, 38, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042889 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042889 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042889/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042889 Building REAL250005042890 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042890' /scratch/stefan/7921153/working/building/REAL250005042890 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042890 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042890/0 /scratch/stefan/7921153/working/building/REAL250005042890 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 1001) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/1001 `/scratch/stefan/7921153/working/3D/1001' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](O)C(=O)N[C@@H]1CCCC[C@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005042890.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042890/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042890 none C[C@H](O)C(=O)N[C@@H]1CCCC[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [26, 20, 26, 26, 20, 20, 12, 12, 12, 12, 12, 12, 12, 5, 12, 5, 1, 5, 1, 1, 1, 1, 1, 1, 26, 26, 26, 78, 20, 12, 12, 12, 12, 12, 12, 12, 12, 6, 1] 78 rigid atoms, others: [38, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 175 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042890 none C[C@H](O)C(=O)N[C@@H]1CCCC[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [15, 6, 15, 15, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 12, 12, 15, 15, 15, 45, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 12] 78 rigid atoms, others: [32, 33, 34, 35, 36, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 38, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 37]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042890 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042890 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042890/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042890 Building REAL250005042891 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042891' /scratch/stefan/7921153/working/building/REAL250005042891 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042891 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042891/0 /scratch/stefan/7921153/working/building/REAL250005042891 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 1002) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/1002 `/scratch/stefan/7921153/working/3D/1002' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC(=O)N[C@@H]1CCCC[C@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005042891.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042891.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042891/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042891 none C=CCC(=O)N[C@@H]1CCCC[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 33, 33, 33, 20, 20, 20, 20, 20, 20, 20, 10, 20, 10, 1, 10, 1, 1, 1, 1, 1, 1, 49, 49, 49, 49, 49, 33, 20, 20, 20, 20, 20, 20, 20, 20, 11, 1] 49 rigid atoms, others: [38, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 177 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042891 none C=CCC(=O)N[C@@H]1CCCC[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [34, 25, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 20, 20, 20, 20, 20, 34, 34, 34, 25, 25, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 20] 49 rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 29, 30, 31] set([0, 1, 2, 3, 4, 37, 38, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042891 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042891 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042891/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042891 Building REAL250005042892 mkdir: created directory `/scratch/stefan/7921153/working/building/REAL250005042892' /scratch/stefan/7921153/working/building/REAL250005042892 /scratch/stefan/7921153/working /scratch/stefan/7921153 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005042892 mkdir: created directory `0' /scratch/stefan/7921153/working/building/REAL250005042892/0 /scratch/stefan/7921153/working/building/REAL250005042892 /scratch/stefan/7921153/working /scratch/stefan/7921153 Protomer 0 (index: 1003) Found valid previously generated 3D confromation in /scratch/stefan/7921153/working/3D/1003 `/scratch/stefan/7921153/working/3D/1003' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CCC(=O)N[C@@H]1CCCC[C@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005042892.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005042892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7921153/working/building/REAL250005042892/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042892 none N#CCC(=O)N[C@@H]1CCCC[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 14, 14, 14, 9, 9, 9, 9, 9, 9, 9, 6, 9, 6, 1, 6, 1, 1, 1, 1, 1, 1, 26, 26, 14, 9, 9, 9, 9, 9, 9, 9, 9, 6, 1] 26 rigid atoms, others: [35, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 91 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005042892 none N#CCC(=O)N[C@@H]1CCCC[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 9, 9, 9, 9, 9, 18, 18, 6, 1, 1, 1, 1, 1, 1, 1, 1, 4, 9] 26 rigid atoms, others: [32, 33, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 35, 34, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7921153/working/building/REAL250005042892 /scratch/stefan/7921153/working /scratch/stefan/7921153 Finished preparing REAL250005042892 Recording results /scratch/stefan/7921153/working /scratch/stefan/7921153 Appending to /scratch/stefan/7921153/finished/xaaaaae.* 0: /scratch/stefan/7921153/working/building/REAL250005042892/0.* Removing working files in /scratch/stefan/7921153/working/building/REAL250005042892 /scratch/stefan/7921153 Compressing combined databse files /scratch/stefan/7921153/finished/xaaaaae.db2.gz /scratch/stefan/7921153/finished/xaaaaae.solv.gz ======================================================= WARNING: STORE_PROTOMERS not executable or a directory! All results left in place (/scratch/stefan/7921153/finished) ======================================================= Finalizing... removed `/scratch/stefan/7921153/working/3D/1004' removed directory: `/scratch/stefan/7921153/working/3D' `/scratch/stefan/7921153/working/protonate' -> `/scratch/stefan/7921153/archive' `/scratch/stefan/7921153/working/input-smiles.ism' -> `/scratch/stefan/7921153/archive/input-smiles.ism' rmdir: removing directory, `/scratch/stefan/7921153/working/building' rmdir: removing directory, `/scratch/stefan/7921153/working' ls: No match. ls: No match.